7C52 | pdb_00007c52

Co-crystal structure of a photosynthetic LH1-RC in complex with electron donor HiPIP

PDB DOI: https://doi.org/10.2210/pdb7C52/pdb

Classification: PHOTOSYNTHESIS
Organism(s): Thermochromatium tepidum
Mutation(s): No
Membrane Protein: Yes OPM PDBTM mpstruc

Deposited: 2020-05-18 Released: 2021-03-03
Deposition Author(s): Yu, L.-J., Wang-Otomo, Z.-Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free:
0.248 (Depositor)
R-Value Work:
0.219 (Depositor)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Crystal structure of a photosynthetic LH1-RC in complex with its electron donor HiPIP.

Kawakami, T., Yu, L.J., Liang, T., Okazaki, K., Madigan, M.T., Kimura, Y., Wang-Otomo, Z.Y.

(2021) Nat Commun 12: 1104-1104

PubMed: 33597527 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-021-21397-9
Primary Citation Related Structures:
7C52

PubMed Abstract:
Photosynthetic electron transfers occur through multiple components ranging from small soluble proteins to large integral membrane protein complexes. Co-crystallization of a bacterial photosynthetic electron transfer complex that employs weak hydrophobic interactions was achieved by using high-molar-ratio mixtures of a soluble donor protein (high-potential iron-sulfur protein, HiPIP) with a membrane-embedded acceptor protein (reaction center, RC) at acidic pH. The structure of the co-complex offers a snapshot of a transient bioenergetic event and revealed a molecular basis for thermodynamically unfavorable interprotein electron tunneling. HiPIP binds to the surface of the tetraheme cytochrome subunit in the light-harvesting (LH1) complex-associated RC in close proximity to the low-potential heme-1 group. The binding interface between the two proteins is primarily formed by uncharged residues and is characterized by hydrophobic features. This co-crystal structure provides a model for the detailed study of long-range trans-protein electron tunneling pathways in biological systems.

Organizational Affiliation

Faculty of Science, Ibaraki University, Mito, Japan.

Macromolecule Content

Total Structure Weight: 424.38 kDa
Atom Count: 27,405
Modeled Residue Count: 2,809
Deposited Residue Count: 2,987
Unique protein chains: 7

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic reaction center cytochrome c subunit	A [auth C]	311	Thermochromatium tepidum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for D2Z0P5 (Thermochromatium tepidum) Explore D2Z0P5 Go to UniProtKB: D2Z0P5
Entity Groups
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UniProt Group	D2Z0P5
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Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic reaction center L subunit	B [auth L]	281	Thermochromatium tepidum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for D2Z0P3 (Thermochromatium tepidum) Explore D2Z0P3 Go to UniProtKB: D2Z0P3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D2Z0P3
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Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic reaction center M subunit	C [auth M]	325	Thermochromatium tepidum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A8ASG6 (Thermochromatium tepidum) Explore A8ASG6 Go to UniProtKB: A8ASG6
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UniProt Group	A8ASG6
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Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic reaction center H subunit	D [auth H]	259	Thermochromatium tepidum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for D2Z0P9 (Thermochromatium tepidum) Explore D2Z0P9 Go to UniProtKB: D2Z0P9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D2Z0P9
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Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
LH1 alpha polypeptide	AA [auth 1] CA [auth 3] E [auth A] EA [auth 5] G [auth D] AA [auth 1], CA [auth 3], E [auth A], EA [auth 5], G [auth D], GA [auth 7], I [auth F], IA [auth 9], K [auth I], M [auth K], O, Q, S, U, W, Y	61	Thermochromatium tepidum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for D2Z0P2 (Thermochromatium tepidum) Explore D2Z0P2 Go to UniProtKB: D2Z0P2
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D2Z0P2
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Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
LH1 beta polypeptide	BA [auth 2] DA [auth 4] F [auth B] FA [auth 6] H [auth E] BA [auth 2], DA [auth 4], F [auth B], FA [auth 6], H [auth E], HA [auth 8], J [auth G], JA [auth 0], L [auth J], N, P, R, T, V, X, Z	47	Thermochromatium tepidum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for D2Z0P1 (Thermochromatium tepidum) Explore D2Z0P1 Go to UniProtKB: D2Z0P1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D2Z0P1
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Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
High-potential iron-sulfur protein	KA [auth b]	83	Thermochromatium tepidum	Mutation(s): 0
UniProt
Find proteins for P80176 (Thermochromatium tepidum) Explore P80176 Go to UniProtKB: P80176
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80176
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Reference Sequence

Small Molecules

Ligands 16 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download:Ideal Coordinates CCD File SDF format, chain DE [auth 1] SDF format, chain FC [auth D] SDF format, chain GC [auth D] SDF format, chain ID [auth S] SDF format, chain JB [auth M] SDF format, chain ND [auth U] SDF format, chain PB [auth M] SDF format, chain WB [auth H] SDF format, chain YD [auth Y] SDF format, chain ZC [auth O] MOL2 format, chain DE [auth 1] MOL2 format, chain FC [auth D] MOL2 format, chain GC [auth D] MOL2 format, chain ID [auth S] MOL2 format, chain JB [auth M] MOL2 format, chain ND [auth U] MOL2 format, chain PB [auth M] MOL2 format, chain WB [auth H] MOL2 format, chain YD [auth Y] MOL2 format, chain ZC [auth O] mmCIF format, chain DE [auth 1] mmCIF format, chain FC [auth D] mmCIF format, chain GC [auth D] mmCIF format, chain ID [auth S] mmCIF format, chain JB [auth M] mmCIF format, chain ND [auth U] mmCIF format, chain PB [auth M] mmCIF format, chain WB [auth H] mmCIF format, chain YD [auth Y] mmCIF format, chain ZC [auth O]	DE [auth 1] FC [auth D] GC [auth D] ID [auth S] JB [auth M] DE [auth 1], FC [auth D], GC [auth D], ID [auth S], JB [auth M], ND [auth U], PB [auth M], WB [auth H], YD [auth Y], ZC [auth O]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain DE [auth 1] Focus chain FC [auth D] Focus chain GC [auth D] Focus chain ID [auth S] Focus chain JB [auth M] Focus chain ND [auth U] Focus chain PB [auth M] Focus chain WB [auth H] Focus chain YD [auth Y] Focus chain ZC [auth O] Interactions & Density Focus chain DE [auth 1] Focus chain FC [auth D] Focus chain GC [auth D] Focus chain ID [auth S] Focus chain JB [auth M] Focus chain ND [auth U] Focus chain PB [auth M] Focus chain WB [auth H] Focus chain YD [auth Y] Focus chain ZC [auth O]
BCL Query on BCL Download:Ideal Coordinates CCD File SDF format, chain AE [auth 1] SDF format, chain BD [auth P] SDF format, chain CC [auth D] SDF format, chain ED [auth Q] SDF format, chain FD [auth S] SDF format, chain GE [auth 2] SDF format, chain HD [auth S] SDF format, chain IC [auth F] SDF format, chain KC [auth F] SDF format, chain KD [auth U] SDF format, chain MC [auth I] SDF format, chain MD [auth U] SDF format, chain NE [auth 4] SDF format, chain OE [auth 5] SDF format, chain PD [auth W] SDF format, chain QC [auth J] SDF format, chain QE [auth 5] SDF format, chain RC [auth K] SDF format, chain RE [auth 7] SDF format, chain SD [auth W] SDF format, chain TA [auth L] SDF format, chain TC [auth K] SDF format, chain TE [auth 7] SDF format, chain UA [auth L] SDF format, chain VD [auth Y] SDF format, chain VE [auth 9] SDF format, chain WC [auth O] SDF format, chain XA [auth L] SDF format, chain XB [auth A] SDF format, chain XD [auth Y] SDF format, chain ZB [auth A] SDF format, chain XE [auth 9] SDF format, chain HE [auth 3] SDF format, chain EC [auth D] SDF format, chain EB [auth M] SDF format, chain CD [auth Q] MOL2 format, chain AE [auth 1] MOL2 format, chain BD [auth P] MOL2 format, chain CC [auth D] MOL2 format, chain ED [auth Q] MOL2 format, chain FD [auth S] MOL2 format, chain GE [auth 2] MOL2 format, chain HD [auth S] MOL2 format, chain IC [auth F] MOL2 format, chain KC [auth F] MOL2 format, chain KD [auth U] MOL2 format, chain MC [auth I] MOL2 format, chain MD [auth U] MOL2 format, chain NE [auth 4] MOL2 format, chain OE [auth 5] MOL2 format, chain PD [auth W] MOL2 format, chain QC [auth J] MOL2 format, chain QE [auth 5] MOL2 format, chain RC [auth K] MOL2 format, chain RE [auth 7] MOL2 format, chain SD [auth W] MOL2 format, chain TA [auth L] MOL2 format, chain TC [auth K] MOL2 format, chain TE [auth 7] MOL2 format, chain UA [auth L] MOL2 format, chain VD [auth Y] MOL2 format, chain VE [auth 9] MOL2 format, chain WC [auth O] MOL2 format, chain XA [auth L] MOL2 format, chain XB [auth A] MOL2 format, chain XD [auth Y] MOL2 format, chain ZB [auth A] MOL2 format, chain XE [auth 9] MOL2 format, chain HE [auth 3] MOL2 format, chain EC [auth D] MOL2 format, chain EB [auth M] MOL2 format, chain CD [auth Q] mmCIF format, chain AE [auth 1] mmCIF format, chain BD [auth P] mmCIF format, chain CC [auth D] mmCIF format, chain ED [auth Q] mmCIF format, chain FD [auth S] mmCIF format, chain GE [auth 2] mmCIF format, chain HD [auth S] mmCIF format, chain IC [auth F] mmCIF format, chain KC [auth F] mmCIF format, chain KD [auth U] mmCIF format, chain MC [auth I] mmCIF format, chain MD [auth U] mmCIF format, chain NE [auth 4] mmCIF format, chain OE [auth 5] mmCIF format, chain PD [auth W] mmCIF format, chain QC [auth J] mmCIF format, chain QE [auth 5] mmCIF format, chain RC [auth K] mmCIF format, chain RE [auth 7] mmCIF format, chain SD [auth W] mmCIF format, chain TA [auth L] mmCIF format, chain TC [auth K] mmCIF format, chain TE [auth 7] mmCIF format, chain UA [auth L] mmCIF format, chain VD [auth Y] mmCIF format, chain VE [auth 9] mmCIF format, chain WC [auth O] mmCIF format, chain XA [auth L] mmCIF format, chain XB [auth A] mmCIF format, chain XD [auth Y] mmCIF format, chain ZB [auth A] mmCIF format, chain XE [auth 9] mmCIF format, chain HE [auth 3] mmCIF format, chain EC [auth D] mmCIF format, chain EB [auth M] mmCIF format, chain CD [auth Q]	AE [auth 1] BD [auth P] CC [auth D] CD [auth Q] EB [auth M] AE [auth 1], BD [auth P], CC [auth D], CD [auth Q], EB [auth M], EC [auth D], ED [auth Q], FD [auth S], GE [auth 2], HD [auth S], HE [auth 3], IC [auth F], KC [auth F], KD [auth U], MC [auth I], MD [auth U], NE [auth 4], OE [auth 5], PD [auth W], QC [auth J], QE [auth 5], RC [auth K], RE [auth 7], SD [auth W], TA [auth L], TC [auth K], TE [auth 7], UA [auth L], VD [auth Y], VE [auth 9], WC [auth O], XA [auth L], XB [auth A], XD [auth Y], XE [auth 9], ZB [auth A]	BACTERIOCHLOROPHYLL A C₅₅ H₇₄ Mg N₄ O₆ DSJXIQQMORJERS-AGGZHOMASA-M		Interactions Focus chain AE [auth 1] Focus chain BD [auth P] Focus chain CC [auth D] Focus chain CD [auth Q] Focus chain EB [auth M] Focus chain EC [auth D] Focus chain ED [auth Q] Focus chain FD [auth S] Focus chain GE [auth 2] Focus chain HD [auth S] Focus chain HE [auth 3] Focus chain IC [auth F] Focus chain KC [auth F] Focus chain KD [auth U] Focus chain MC [auth I] Focus chain MD [auth U] Focus chain NE [auth 4] Focus chain OE [auth 5] Focus chain PD [auth W] Focus chain QC [auth J] Focus chain QE [auth 5] Focus chain RC [auth K] Focus chain RE [auth 7] Focus chain SD [auth W] Focus chain TA [auth L] Focus chain TC [auth K] Focus chain TE [auth 7] Focus chain UA [auth L] Focus chain VD [auth Y] Focus chain VE [auth 9] Focus chain WC [auth O] Focus chain XA [auth L] Focus chain XB [auth A] Focus chain XD [auth Y] Focus chain XE [auth 9] Focus chain ZB [auth A] Interactions & Density Focus chain AE [auth 1] Focus chain BD [auth P] Focus chain CC [auth D] Focus chain CD [auth Q] Focus chain EB [auth M] Focus chain EC [auth D] Focus chain ED [auth Q] Focus chain FD [auth S] Focus chain GE [auth 2] Focus chain HD [auth S] Focus chain HE [auth 3] Focus chain IC [auth F] Focus chain KC [auth F] Focus chain KD [auth U] Focus chain MC [auth I] Focus chain MD [auth U] Focus chain NE [auth 4] Focus chain OE [auth 5] Focus chain PD [auth W] Focus chain QC [auth J] Focus chain QE [auth 5] Focus chain RC [auth K] Focus chain RE [auth 7] Focus chain SD [auth W] Focus chain TA [auth L] Focus chain TC [auth K] Focus chain TE [auth 7] Focus chain UA [auth L] Focus chain VD [auth Y] Focus chain VE [auth 9] Focus chain WC [auth O] Focus chain XA [auth L] Focus chain XB [auth A] Focus chain XD [auth Y] Focus chain XE [auth 9] Focus chain ZB [auth A]
BPH Query on BPH Download:Ideal Coordinates CCD File SDF format, chain FB [auth M] SDF format, chain VA [auth L] MOL2 format, chain FB [auth M] MOL2 format, chain VA [auth L] mmCIF format, chain FB [auth M] mmCIF format, chain VA [auth L]	FB [auth M], VA [auth L]	BACTERIOPHEOPHYTIN A C₅₅ H₇₆ N₄ O₆ KWOZSBGNAHVCKG-SZQBJALDSA-N		Interactions Focus chain FB [auth M] Focus chain VA [auth L] Interactions & Density Focus chain FB [auth M] Focus chain VA [auth L]
PGV Query on PGV Download:Ideal Coordinates CCD File SDF format, chain AB [auth L] SDF format, chain EE [auth 1] SDF format, chain HC [auth D] SDF format, chain NB [auth M] SDF format, chain UB [auth H] SDF format, chain YE [auth 9] SDF format, chain ZA [auth L] SDF format, chain SA [auth C] SDF format, chain OB [auth M] SDF format, chain LE [auth 3] MOL2 format, chain AB [auth L] MOL2 format, chain EE [auth 1] MOL2 format, chain HC [auth D] MOL2 format, chain NB [auth M] MOL2 format, chain UB [auth H] MOL2 format, chain YE [auth 9] MOL2 format, chain ZA [auth L] MOL2 format, chain SA [auth C] MOL2 format, chain OB [auth M] MOL2 format, chain LE [auth 3] mmCIF format, chain AB [auth L] mmCIF format, chain EE [auth 1] mmCIF format, chain HC [auth D] mmCIF format, chain NB [auth M] mmCIF format, chain UB [auth H] mmCIF format, chain YE [auth 9] mmCIF format, chain ZA [auth L] mmCIF format, chain SA [auth C] mmCIF format, chain OB [auth M] mmCIF format, chain LE [auth 3]	AB [auth L] EE [auth 1] HC [auth D] LE [auth 3] NB [auth M] AB [auth L], EE [auth 1], HC [auth D], LE [auth 3], NB [auth M], OB [auth M], SA [auth C], UB [auth H], YE [auth 9], ZA [auth L]	(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE C₄₀ H₇₇ O₁₀ P ADYWCMPUNIVOEA-GPJPVTGXSA-N		Interactions Focus chain AB [auth L] Focus chain EE [auth 1] Focus chain HC [auth D] Focus chain LE [auth 3] Focus chain NB [auth M] Focus chain OB [auth M] Focus chain SA [auth C] Focus chain UB [auth H] Focus chain YE [auth 9] Focus chain ZA [auth L] Interactions & Density Focus chain AB [auth L] Focus chain EE [auth 1] Focus chain HC [auth D] Focus chain LE [auth 3] Focus chain NB [auth M] Focus chain OB [auth M] Focus chain SA [auth C] Focus chain UB [auth H] Focus chain YE [auth 9] Focus chain ZA [auth L]
UQ8 Query on UQ8 Download:Ideal Coordinates CCD File SDF format, chain BB [auth L] SDF format, chain CB [auth L] SDF format, chain QB [auth M] SDF format, chain WA [auth L] SDF format, chain DB [auth L] MOL2 format, chain BB [auth L] MOL2 format, chain CB [auth L] MOL2 format, chain QB [auth M] MOL2 format, chain WA [auth L] MOL2 format, chain DB [auth L] mmCIF format, chain BB [auth L] mmCIF format, chain CB [auth L] mmCIF format, chain QB [auth M] mmCIF format, chain WA [auth L] mmCIF format, chain DB [auth L]	BB [auth L], CB [auth L], DB [auth L], QB [auth M], WA [auth L]	Ubiquinone-8 C₄₉ H₇₄ O₄ ICFIZJQGJAJRSU-SGHXUWJISA-N		Interactions Focus chain BB [auth L] Focus chain CB [auth L] Focus chain DB [auth L] Focus chain QB [auth M] Focus chain WA [auth L] Interactions & Density Focus chain BB [auth L] Focus chain CB [auth L] Focus chain DB [auth L] Focus chain QB [auth M] Focus chain WA [auth L]
LHG Query on LHG Download:Ideal Coordinates CCD File SDF format, chain RA [auth C] MOL2 format, chain RA [auth C] mmCIF format, chain RA [auth C]	RA [auth C]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C₃₈ H₇₅ O₁₀ P BIABMEZBCHDPBV-MPQUPPDSSA-N		Interactions Focus chain RA [auth C] Interactions & Density Focus chain RA [auth C]
MQ8 Query on MQ8 Download:Ideal Coordinates CCD File SDF format, chain HB [auth M] MOL2 format, chain HB [auth M] mmCIF format, chain HB [auth M]	HB [auth M]	MENAQUINONE 8 C₅₁ H₇₂ O₂ LXKDFTDVRVLXFY-ACMRXAIVSA-N		Interactions Focus chain HB [auth M] Interactions & Density Focus chain HB [auth M]
PEF Query on PEF Download:Ideal Coordinates CCD File SDF format, chain KE [auth 3] SDF format, chain LB [auth M] SDF format, chain MB [auth M] SDF format, chain TD [auth W] SDF format, chain UC [auth K] SDF format, chain UD [auth W] SDF format, chain TB [auth H] SDF format, chain OC [auth I] SDF format, chain KB [auth M] SDF format, chain CE [auth 1] MOL2 format, chain KE [auth 3] MOL2 format, chain LB [auth M] MOL2 format, chain MB [auth M] MOL2 format, chain TD [auth W] MOL2 format, chain UC [auth K] MOL2 format, chain UD [auth W] MOL2 format, chain TB [auth H] MOL2 format, chain OC [auth I] MOL2 format, chain KB [auth M] MOL2 format, chain CE [auth 1] mmCIF format, chain KE [auth 3] mmCIF format, chain LB [auth M] mmCIF format, chain MB [auth M] mmCIF format, chain TD [auth W] mmCIF format, chain UC [auth K] mmCIF format, chain UD [auth W] mmCIF format, chain TB [auth H] mmCIF format, chain OC [auth I] mmCIF format, chain KB [auth M] mmCIF format, chain CE [auth 1]	CE [auth 1] KB [auth M] KE [auth 3] LB [auth M] MB [auth M] CE [auth 1], KB [auth M], KE [auth 3], LB [auth M], MB [auth M], OC [auth I], TB [auth H], TD [auth W], UC [auth K], UD [auth W]	DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE C₃₇ H₇₄ N O₈ P SLKDGVPOSSLUAI-PGUFJCEWSA-N		Interactions Focus chain CE [auth 1] Focus chain KB [auth M] Focus chain KE [auth 3] Focus chain LB [auth M] Focus chain MB [auth M] Focus chain OC [auth I] Focus chain TB [auth H] Focus chain TD [auth W] Focus chain UC [auth K] Focus chain UD [auth W] Interactions & Density Focus chain CE [auth 1] Focus chain KB [auth M] Focus chain KE [auth 3] Focus chain LB [auth M] Focus chain MB [auth M] Focus chain OC [auth I] Focus chain TB [auth H] Focus chain TD [auth W] Focus chain UC [auth K] Focus chain UD [auth W]
HEC (Subject of Investigation/LOI) Query on HEC Download:Ideal Coordinates CCD File SDF format, chain MA [auth C] SDF format, chain NA [auth C] SDF format, chain OA [auth C] SDF format, chain LA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain LA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain NA [auth C] mmCIF format, chain OA [auth C] mmCIF format, chain LA [auth C]	LA [auth C], MA [auth C], NA [auth C], OA [auth C]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Interactions & Density Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C]
CRT Query on CRT Download:Ideal Coordinates CCD File SDF format, chain AD [auth P] SDF format, chain BC [auth B] SDF format, chain FE [auth 2] SDF format, chain JE [auth 3] SDF format, chain ME [auth 4] SDF format, chain OD [auth V] SDF format, chain UE [auth 8] SDF format, chain ZD [auth Z] SDF format, chain ZE [auth 0] SDF format, chain YC [auth O] SDF format, chain VC [auth N] SDF format, chain QD [auth W] SDF format, chain PC [auth J] SDF format, chain LC [auth G] SDF format, chain JD [auth T] SDF format, chain IB [auth M] SDF format, chain AC [auth A] MOL2 format, chain AD [auth P] MOL2 format, chain BC [auth B] MOL2 format, chain FE [auth 2] MOL2 format, chain JE [auth 3] MOL2 format, chain ME [auth 4] MOL2 format, chain OD [auth V] MOL2 format, chain UE [auth 8] MOL2 format, chain ZD [auth Z] MOL2 format, chain ZE [auth 0] MOL2 format, chain YC [auth O] MOL2 format, chain VC [auth N] MOL2 format, chain QD [auth W] MOL2 format, chain PC [auth J] MOL2 format, chain LC [auth G] MOL2 format, chain JD [auth T] MOL2 format, chain IB [auth M] MOL2 format, chain AC [auth A] mmCIF format, chain AD [auth P] mmCIF format, chain BC [auth B] mmCIF format, chain FE [auth 2] mmCIF format, chain JE [auth 3] mmCIF format, chain ME [auth 4] mmCIF format, chain OD [auth V] mmCIF format, chain UE [auth 8] mmCIF format, chain ZD [auth Z] mmCIF format, chain ZE [auth 0] mmCIF format, chain YC [auth O] mmCIF format, chain VC [auth N] mmCIF format, chain QD [auth W] mmCIF format, chain PC [auth J] mmCIF format, chain LC [auth G] mmCIF format, chain JD [auth T] mmCIF format, chain IB [auth M] mmCIF format, chain AC [auth A]	AC [auth A] AD [auth P] BC [auth B] FE [auth 2] IB [auth M] AC [auth A], AD [auth P], BC [auth B], FE [auth 2], IB [auth M], JD [auth T], JE [auth 3], LC [auth G], ME [auth 4], OD [auth V], PC [auth J], QD [auth W], UE [auth 8], VC [auth N], YC [auth O], ZD [auth Z], ZE [auth 0]	SPIRILLOXANTHIN C₄₂ H₆₀ O₂ VAZQBTJCYODOSV-RISZBRKMSA-N		Interactions Focus chain AC [auth A] Focus chain AD [auth P] Focus chain BC [auth B] Focus chain FE [auth 2] Focus chain IB [auth M] Focus chain JD [auth T] Focus chain JE [auth 3] Focus chain LC [auth G] Focus chain ME [auth 4] Focus chain OD [auth V] Focus chain PC [auth J] Focus chain QD [auth W] Focus chain UE [auth 8] Focus chain VC [auth N] Focus chain YC [auth O] Focus chain ZD [auth Z] Focus chain ZE [auth 0] Interactions & Density Focus chain AC [auth A] Focus chain AD [auth P] Focus chain BC [auth B] Focus chain FE [auth 2] Focus chain IB [auth M] Focus chain JD [auth T] Focus chain JE [auth 3] Focus chain LC [auth G] Focus chain ME [auth 4] Focus chain OD [auth V] Focus chain PC [auth J] Focus chain QD [auth W] Focus chain UE [auth 8] Focus chain VC [auth N] Focus chain YC [auth O] Focus chain ZD [auth Z] Focus chain ZE [auth 0]
LMT Query on LMT Download:Ideal Coordinates CCD File SDF format, chain VB [auth H] SDF format, chain RB [auth M] MOL2 format, chain VB [auth H] MOL2 format, chain RB [auth M] mmCIF format, chain VB [auth H] mmCIF format, chain RB [auth M]	RB [auth M], VB [auth H]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain RB [auth M] Focus chain VB [auth H] Interactions & Density Focus chain RB [auth M] Focus chain VB [auth H]
SF4 (Subject of Investigation/LOI) Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain AF [auth b] MOL2 format, chain AF [auth b] mmCIF format, chain AF [auth b]	AF [auth b]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain AF [auth b] Interactions & Density Focus chain AF [auth b]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain YA [auth L] MOL2 format, chain YA [auth L] mmCIF format, chain YA [auth L]	YA [auth L]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain YA [auth L] Interactions & Density Focus chain YA [auth L]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain SB [auth H] SDF format, chain QA [auth C] MOL2 format, chain SB [auth H] MOL2 format, chain QA [auth C] mmCIF format, chain SB [auth H] mmCIF format, chain QA [auth C]	QA [auth C], SB [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain QA [auth C] Focus chain SB [auth H] Interactions & Density Focus chain QA [auth C] Focus chain SB [auth H]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain GB [auth M] MOL2 format, chain GB [auth M] mmCIF format, chain GB [auth M]	GB [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain GB [auth M] Interactions & Density Focus chain GB [auth M]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain DC [auth D] SDF format, chain GD [auth S] SDF format, chain IE [auth 3] SDF format, chain NC [auth I] SDF format, chain SC [auth K] SDF format, chain WE [auth 9] SDF format, chain YB [auth A] SDF format, chain XC [auth O] SDF format, chain WD [auth Y] SDF format, chain SE [auth 7] SDF format, chain RD [auth W] SDF format, chain PE [auth 5] SDF format, chain PA [auth C] SDF format, chain LD [auth U] SDF format, chain JC [auth F] SDF format, chain DD [auth Q] SDF format, chain BE [auth 1] MOL2 format, chain DC [auth D] MOL2 format, chain GD [auth S] MOL2 format, chain IE [auth 3] MOL2 format, chain NC [auth I] MOL2 format, chain SC [auth K] MOL2 format, chain WE [auth 9] MOL2 format, chain YB [auth A] MOL2 format, chain XC [auth O] MOL2 format, chain WD [auth Y] MOL2 format, chain SE [auth 7] MOL2 format, chain RD [auth W] MOL2 format, chain PE [auth 5] MOL2 format, chain PA [auth C] MOL2 format, chain LD [auth U] MOL2 format, chain JC [auth F] MOL2 format, chain DD [auth Q] MOL2 format, chain BE [auth 1] mmCIF format, chain DC [auth D] mmCIF format, chain GD [auth S] mmCIF format, chain IE [auth 3] mmCIF format, chain NC [auth I] mmCIF format, chain SC [auth K] mmCIF format, chain WE [auth 9] mmCIF format, chain YB [auth A] mmCIF format, chain XC [auth O] mmCIF format, chain WD [auth Y] mmCIF format, chain SE [auth 7] mmCIF format, chain RD [auth W] mmCIF format, chain PE [auth 5] mmCIF format, chain PA [auth C] mmCIF format, chain LD [auth U] mmCIF format, chain JC [auth F] mmCIF format, chain DD [auth Q] mmCIF format, chain BE [auth 1]	BE [auth 1] DC [auth D] DD [auth Q] GD [auth S] IE [auth 3] BE [auth 1], DC [auth D], DD [auth Q], GD [auth S], IE [auth 3], JC [auth F], LD [auth U], NC [auth I], PA [auth C], PE [auth 5], RD [auth W], SC [auth K], SE [auth 7], WD [auth Y], WE [auth 9], XC [auth O], YB [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain BE [auth 1] Focus chain DC [auth D] Focus chain DD [auth Q] Focus chain GD [auth S] Focus chain IE [auth 3] Focus chain JC [auth F] Focus chain LD [auth U] Focus chain NC [auth I] Focus chain PA [auth C] Focus chain PE [auth 5] Focus chain RD [auth W] Focus chain SC [auth K] Focus chain SE [auth 7] Focus chain WD [auth Y] Focus chain WE [auth 9] Focus chain XC [auth O] Focus chain YB [auth A] Interactions & Density Focus chain BE [auth 1] Focus chain DC [auth D] Focus chain DD [auth Q] Focus chain GD [auth S] Focus chain IE [auth 3] Focus chain JC [auth F] Focus chain LD [auth U] Focus chain NC [auth I] Focus chain PA [auth C] Focus chain PE [auth 5] Focus chain RD [auth W] Focus chain SC [auth K] Focus chain SE [auth 7] Focus chain WD [auth Y] Focus chain WE [auth 9] Focus chain XC [auth O] Focus chain YB [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free: 0.248 (Depositor)
R-Value Work: 0.219 (Depositor)
R-Value Observed: 0.220 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.435	α = 90
b = 183.335	β = 112.584
c = 123.857	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building
PHENIX	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2021-03-03

Deposition Author(s):

Yu, L.-J.

Wang-Otomo, Z.-Y.

Revision History (Full details and data files)

Version 1.0: 2021-03-03
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, Refinement description
Version 1.2: 2025-09-17
Changes: Advisory, Derived calculations, Structure summary
Version 2.0: 2025-12-17
Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

7C52 | pdb_00007c52

Co-crystal structure of a photosynthetic LH1-RC in complex with electron donor HiPIP

Literature

Crystal structure of a photosynthetic LH1-RC in complex with its electron donor HiPIP.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

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Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)