8YW3

Cryo-EM structure of the retatrutide-bound human GLP-1R-Gs complex

PDB DOI: https://doi.org/10.2210/pdb8YW3/pdb
EM Map EMD-39621: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): synthetic construct, Homo sapiens
Expression System: Escherichia coli, Spodoptera frugiperda
Mutation(s): Yes
Membrane Protein: Yes PDBTMmpstruc

Deposited: 2024-03-29 Released: 2024-09-18
Deposition Author(s): Li, W.Z., Zhou, Q.T., Cong, Z.T., Yuan, Q.N., Li, W.X., Zhao, F.H., Xu, H.E., Zhao, L.H., Yang, D.H., Wang, M.W.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.68 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural insights into the triple agonism at GLP-1R, GIPR and GCGR manifested by retatrutide.

Li, W., Zhou, Q., Cong, Z., Yuan, Q., Li, W., Zhao, F., Xu, H.E., Zhao, L.H., Yang, D., Wang, M.W.

(2024) Cell Discov 10: 77-77

PubMed: 39019866 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41421-024-00700-0
Primary Citation of Related Structures:
8YW3, 8YW4, 8YW5

Organizational Affiliation

State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.

Macromolecule Content

Total Structure Weight: 161.02 kDa
Atom Count: 9,231
Modelled Residue Count: 1,160
Deposited Residue Count: 1,420
Unique protein chains: 6

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody-35	A [auth N]	140	synthetic construct	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: 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(s) subunit alpha isoforms short	C [auth A]	394	Homo sapiens	Mutation(s): 8 Gene Names: GNAS, GNAS1, GSP EC: 3.6.5 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P63092 (Homo sapiens) Explore P63092 Go to UniProtKB: P63092
PHAROS: P63092 GTEx: ENSG00000087460
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63092
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucagon-like peptide 1 receptor	D [auth R]	440	Homo sapiens	Mutation(s): 0 Gene Names: GLP1R Membrane Entity: Yes
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

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	E [auth G]	71	Homo sapiens	Mutation(s): 0 Gene Names: GNG2 Membrane Entity: Yes
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: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Retatrutide	F [auth P]	30	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
2ML Query on 2ML	F [auth P]	L-PEPTIDE LINKING	C₇ H₁₅ N O₂		LEU
AIB Query on AIB	F [auth P]	L-PEPTIDE LINKING	C₄ H₉ N O₂		ALA

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.68 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-09-18

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
National Natural Science Foundation of China (NSFC)	China	82273985
National Natural Science Foundation of China (NSFC)	China	82121005
National Natural Science Foundation of China (NSFC)	China	81973373
National Natural Science Foundation of China (NSFC)	China	32200576 (Z.T.C.), 32071203(L.H.Z), 82121005(H.E.X.) and 82204474 (F.H.Z.); National Science and Technology Major