9IVM | pdb_00009ivm

Cryo-EM structure of the GLP-1(9-36)-bound human GLP-1R-Gs complex in the presence of LSN3318839

PDB DOI: https://doi.org/10.2210/pdb9IVM/pdb
EM Map EMD-60930: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2024-07-24 Released: 2024-11-13
Deposition Author(s): Li, J., Li, G., Mai, Y., Liu, X., Yang, D., Zhou, Q., Wang, M.-W.
Funding Organization(s): National Natural Science Foundation of China (NSFC), Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.22 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Molecular basis of enhanced GLP-1 signaling mediated by GLP-1(9-36) in conjunction with LSN3318839.

Li, J., Li, G., Mai, Y., Liu, X., Yang, D., Zhou, Q., Wang, M.W.

(2024) Acta Pharm Sin B 14: 5069-5073

PubMed: 39664415 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1016/j.apsb.2024.09.002
Primary Citation of Related Structures:
9IVG, 9IVM

Organizational Affiliation

Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.

Macromolecule Content

Total Structure Weight: 157.3 kDa
Atom Count: 9,390
Modeled Residue Count: 1,177
Deposited Residue Count: 1,384
Unique protein chains: 6

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short	A	361	Homo sapiens	Mutation(s): 0 Gene Names: GNAI1, GNAS, GNAS1, GSP EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P63092 (Homo sapiens) Explore P63092 Go to UniProtKB: P63092
PHAROS: P63092 GTEx: ENSG00000087460
Find proteins for P63096 (Homo sapiens) Explore P63096 Go to UniProtKB: P63096
PHAROS: P63096 GTEx: ENSG00000127955
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P63096P63092
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	345	Homo sapiens	Mutation(s): 0 Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens) Explore P62873 Go to UniProtKB: P62873
PHAROS: P62873 GTEx: ENSG00000078369
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62873
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C [auth G]	70	Homo sapiens	Mutation(s): 0 Gene Names: GNG2
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens) Explore P59768 Go to UniProtKB: P59768
PHAROS: P59768 GTEx: ENSG00000186469
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P59768
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody-35	D [auth N]	140	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
GLP-1(9-36)	E [auth P]	28	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucagon-like peptide 1 receptor	F [auth R]	440	Homo sapiens	Mutation(s): 0 Gene Names: GLP1R
UniProt & NIH Common Fund Data Resources
Find proteins for P43220 (Homo sapiens) Explore P43220 Go to UniProtKB: P43220
PHAROS: P43220 GTEx: ENSG00000112164
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P43220
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1EEC (Subject of Investigation/LOI) Query on A1EEC Download Ideal Coordinates CCD File SDF format, chain G [auth R] MOL2 format, chain G [auth R] mmCIF format, chain G [auth R]	G [auth R]	(2~{R})-2-[2-[1-[(1~{R})-1-[2,6-bis(chloranyl)-3-cyclopropyl-phenyl]ethyl]imidazo[4,5-c]pyridin-6-yl]phenyl]propanoic acid C₂₆ H₂₃ Cl₂ N₃ O₂ JPJWHCNGSBCZMI-HUUCEWRRSA-N		Interactions Focus chain G [auth R] Interactions & Density Focus chain G [auth R]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.22 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-11-13

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82273961
National Natural Science Foundation of China (NSFC)	China	82073904
National Natural Science Foundation of China (NSFC)	China	81872915
Other government		2021ZD0203400
Other government		ZDKJ2021028