8ZRK | pdb_00008zrk

Cryo-EM structure of GPR119-Gs Complex with small molecule agonist GSK-1292263

PDB DOI: https://doi.org/10.2210/pdb8ZRK/pdb
EM Map EMD-60399: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, synthetic construct
Expression System: Spodoptera frugiperda, Escherichia coli
Mutation(s): No

Deposited: 2024-06-04 Released: 2024-06-19
Deposition Author(s): Wong, T.S., Xiong, T.T., Zeng, Z.C., Gan, S.Y., Qiu, C., Du, Y.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.82 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

Cryo-EM structure of GPR119-Gs complex

Wong, T.S., Xiong, T.T., Zeng, Z.C.

To be published.

Macromolecule Content

Total Structure Weight: 154.42 kDa
Atom Count: 8,018
Modeled Residue Count: 1,032
Deposited Residue Count: 1,375
Unique protein chains: 5

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short	A	394	Homo sapiens	Mutation(s): 0 Gene Names: 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63092
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	384	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62873
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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]	71	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P59768
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
nanobody35	D [auth N]	157	synthetic construct	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-dependent insulinotropic receptor	E [auth R]	369	Homo sapiens	Mutation(s): 0 Gene Names: GPR119
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TDV5 (Homo sapiens) Explore Q8TDV5 Go to UniProtKB: Q8TDV5
PHAROS: Q8TDV5 GTEx: ENSG00000147262
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8TDV5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1D8Y (Subject of Investigation/LOI) Query on A1D8Y Download:Ideal Coordinates CCD File SDF format, chain F [auth R] MOL2 format, chain F [auth R] mmCIF format, chain F [auth R]	F [auth R]	GSK-1292263 C₂₃ H₂₈ N₄ O₄ S AYJRTVVIBJSSKN-UHFFFAOYSA-N		Interactions Focus chain F [auth R] Interactions & Density Focus chain F [auth R]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.82 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-06-19

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-06-19
Type: Initial release
Version 1.1: 2024-11-20
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2025-07-16
Changes: Data collection