9U40 | pdb_00009u40

Cryo-EM structure of peptide GPCR-Gq complex

• PDB DOI: https://doi.org/10.2210/pdb9U40/pdb
• EM Map EMD-63831: EMDB EMDataResource

• Classification: SIGNALING PROTEIN/IMMUNE SYSTEM
• Organism(s): Clostridium perfringens, Homo sapiens, Lama glama
• Expression System: Trichoplusia ni, Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-03-19 Released: 2026-09-23 
• Deposition Author(s): Liu, S.H., Zhang, Y.J., Hua, T., Liu, Z.J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.04 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of peptide GPCR-Gq complex

Liu, S.H., Zhang, Y.J., Hua, T., Liu, Z.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A1B1C1D1E1F1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 191.11 kDa 
• Atom Count: 8,211 
• Modeled Residue Count: 1,042 
• Deposited Residue Count: 1,716 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
exo-alpha-sialidase,Vasopressin V1a receptor	A [auth R]	855	Clostridium perfringens, Homo sapiens This entity is chimeric	Mutation(s): 0  Gene Names: nanH, AVPR1A, AVPR1 EC: 3.2.1.18
UniProt & NIH Common Fund Data Resources
Find proteins for Q59310 (Clostridium perfringens) Explore Q59310  Go to UniProtKB:  Q59310
Find proteins for P37288 (Homo sapiens) Explore P37288  Go to UniProtKB:  P37288
PHAROS:  P37288 GTEx:  ENSG00000166148
UniProt Groups	P37288Q59310

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Arg-vasopressin	B [auth P]	10	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P01185 (Homo sapiens) Explore P01185  Go to UniProtKB:  P01185
PHAROS:  P01185 GTEx:  ENSG00000101200

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(q) subunit alpha-1	C [auth A]	246	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	D [auth B]	377	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 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
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens) Explore P59768  Go to UniProtKB:  P59768
PHAROS:  P59768 GTEx:  ENSG00000186469

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody 35	F [auth N]	157	Lama glama	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG (Subject of Investigation/LOI)	G [auth R]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.04 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-23 
Deposition Author(s): Liu, S.H., Zhang, Y.J., Hua, T., Liu, Z.J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-09-23
  Type: Initial release