9J99 | pdb_00009j99

Substrate-engaged TOM complex from yeast

PDB DOI: https://doi.org/10.2210/pdb9J99/pdb
EM Map EMD-61256: EMDB EMDataResource

Classification: PROTEIN TRANSPORT
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Saccharomyces cerevisiae
Mutation(s): No
Membrane Protein: Yes MemProtMD

Deposited: 2024-08-22 Released: 2025-09-10
Deposition Author(s): Yang, Y.Q., Wang, G.P.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.94 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Substrate-engaged TOM complex from yeast

Yang, Y.Q., Wang, G.P.

To be published.

Macromolecule Content

Total Structure Weight: 180.13 kDa
Atom Count: 8,859
Modeled Residue Count: 980
Deposited Residue Count: 1,420
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial import receptor subunit TOM40	A, F [auth I]	387	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: TOM40, ISP42, MOM38, YMR203W, YM8325.04 Membrane Entity: Yes
UniProt
Find proteins for P23644 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P23644 Go to UniProtKB: P23644
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P23644
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial import receptor subunit TOM22	B, G [auth J]	152	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: TOM22, MAS17, MAS22, MOM22, YNL131W, N1217, N1862 Membrane Entity: Yes
UniProt
Find proteins for P49334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P49334 Go to UniProtKB: P49334
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49334
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial import receptor subunit TOM5	C, H [auth K]	50	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: TOM5, MOM8A, YPR133W-A Membrane Entity: Yes
UniProt
Find proteins for P80967 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P80967 Go to UniProtKB: P80967
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P80967
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial import receptor subunit TOM6	D, I [auth L]	61	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: TOM6, ISP6, YOR045W Membrane Entity: Yes
UniProt
Find proteins for P33448 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P33448 Go to UniProtKB: P33448
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P33448
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial import receptor subunit TOM7	E, J [auth M]	60	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: TOM7, MOM7, YNL070W, N2378 Membrane Entity: Yes
UniProt
Find proteins for P53507 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53507 Go to UniProtKB: P53507
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P53507
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PC1 Query on PC1 Download Ideal Coordinates CCD File SDF format, chain AB [auth L] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain FB [auth M] SDF format, chain JA [auth E] SDF format, chain L [auth A] SDF format, chain LA [auth I] SDF format, chain M [auth A] SDF format, chain MA [auth I] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain PA [auth I] SDF format, chain QA [auth I] SDF format, chain S [auth A] SDF format, chain SA [auth I] SDF format, chain TA [auth I] SDF format, chain U [auth A] SDF format, chain UA [auth I] SDF format, chain V [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain ZA [auth J] SDF format, chain YA [auth J] SDF format, chain NA [auth I] MOL2 format, chain AB [auth L] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FB [auth M] MOL2 format, chain JA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth I] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth I] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain PA [auth I] MOL2 format, chain QA [auth I] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth I] MOL2 format, chain TA [auth I] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth I] MOL2 format, chain V [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain ZA [auth J] MOL2 format, chain YA [auth J] MOL2 format, chain NA [auth I] mmCIF format, chain AB [auth L] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain FB [auth M] mmCIF format, chain JA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth I] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth I] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain PA [auth I] mmCIF format, chain QA [auth I] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth I] mmCIF format, chain TA [auth I] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth I] mmCIF format, chain V [auth A] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain ZA [auth J] mmCIF format, chain YA [auth J] mmCIF format, chain NA [auth I]	AB [auth L] CA [auth D] DA [auth D] EA [auth D] FB [auth M] AB [auth L], CA [auth D], DA [auth D], EA [auth D], FB [auth M], JA [auth E], L [auth A], LA [auth I], M [auth A], MA [auth I], N [auth A], NA [auth I], O [auth A], PA [auth I], QA [auth I], S [auth A], SA [auth I], TA [auth I], U [auth A], UA [auth I], V [auth A], X [auth B], Y [auth B], YA [auth J], ZA [auth J]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₈ N O₈ P NRJAVPSFFCBXDT-HUESYALOSA-N		Interactions Focus chain AB [auth L] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FB [auth M] Focus chain JA [auth E] Focus chain L [auth A] Focus chain LA [auth I] Focus chain M [auth A] Focus chain MA [auth I] Focus chain N [auth A] Focus chain NA [auth I] Focus chain O [auth A] Focus chain PA [auth I] Focus chain QA [auth I] Focus chain S [auth A] Focus chain SA [auth I] Focus chain TA [auth I] Focus chain U [auth A] Focus chain UA [auth I] Focus chain V [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain YA [auth J] Focus chain ZA [auth J] Interactions & Density Focus chain AB [auth L] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FB [auth M] Focus chain JA [auth E] Focus chain L [auth A] Focus chain LA [auth I] Focus chain M [auth A] Focus chain MA [auth I] Focus chain N [auth A] Focus chain NA [auth I] Focus chain O [auth A] Focus chain PA [auth I] Focus chain QA [auth I] Focus chain S [auth A] Focus chain SA [auth I] Focus chain TA [auth I] Focus chain U [auth A] Focus chain UA [auth I] Focus chain V [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain YA [auth J] Focus chain ZA [auth J]
UND (Subject of Investigation/LOI) Query on UND Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth D] SDF format, chain BB [auth L] SDF format, chain CB [auth L] SDF format, chain DB [auth L] SDF format, chain EB [auth M] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain GB [auth M] SDF format, chain HA [auth E] SDF format, chain HB [auth M] SDF format, chain IA [auth E] SDF format, chain IB [auth M] SDF format, chain K [auth A] SDF format, chain KA [auth E] SDF format, chain OA [auth I] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain RA [auth I] SDF format, chain T [auth A] SDF format, chain VA [auth I] SDF format, chain W [auth B] SDF format, chain WA [auth I] SDF format, chain XA [auth I] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain BB [auth L] MOL2 format, chain CB [auth L] MOL2 format, chain DB [auth L] MOL2 format, chain EB [auth M] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain GB [auth M] MOL2 format, chain HA [auth E] MOL2 format, chain HB [auth M] MOL2 format, chain IA [auth E] MOL2 format, chain IB [auth M] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain OA [auth I] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth I] MOL2 format, chain T [auth A] MOL2 format, chain VA [auth I] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth I] MOL2 format, chain XA [auth I] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain BB [auth L] mmCIF format, chain CB [auth L] mmCIF format, chain DB [auth L] mmCIF format, chain EB [auth M] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain GB [auth M] mmCIF format, chain HA [auth E] mmCIF format, chain HB [auth M] mmCIF format, chain IA [auth E] mmCIF format, chain IB [auth M] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth E] mmCIF format, chain OA [auth I] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth I] mmCIF format, chain T [auth A] mmCIF format, chain VA [auth I] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth I] mmCIF format, chain XA [auth I] mmCIF format, chain Z [auth C]	AA [auth C] BA [auth D] BB [auth L] CB [auth L] DB [auth L] AA [auth C], BA [auth D], BB [auth L], CB [auth L], DB [auth L], EB [auth M], FA [auth D], GA [auth D], GB [auth M], HA [auth E], HB [auth M], IA [auth E], IB [auth M], K [auth A], KA [auth E], OA [auth I], P [auth A], Q [auth A], R [auth A], RA [auth I], T [auth A], VA [auth I], W [auth B], WA [auth I], XA [auth I], Z [auth C]	UNDECANE C₁₁ H₂₄ RSJKGSCJYJTIGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth D] Focus chain BB [auth L] Focus chain CB [auth L] Focus chain DB [auth L] Focus chain EB [auth M] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain GB [auth M] Focus chain HA [auth E] Focus chain HB [auth M] Focus chain IA [auth E] Focus chain IB [auth M] Focus chain K [auth A] Focus chain KA [auth E] Focus chain OA [auth I] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain RA [auth I] Focus chain T [auth A] Focus chain VA [auth I] Focus chain W [auth B] Focus chain WA [auth I] Focus chain XA [auth I] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth D] Focus chain BB [auth L] Focus chain CB [auth L] Focus chain DB [auth L] Focus chain EB [auth M] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain GB [auth M] Focus chain HA [auth E] Focus chain HB [auth M] Focus chain IA [auth E] Focus chain IB [auth M] Focus chain K [auth A] Focus chain KA [auth E] Focus chain OA [auth I] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain RA [auth I] Focus chain T [auth A] Focus chain VA [auth I] Focus chain W [auth B] Focus chain WA [auth I] Focus chain XA [auth I] Focus chain Z [auth C]