9KPF | pdb_00009kpf

Cryo-EM structure of GPCR16-Gi complex

• PDB DOI: https://doi.org/10.2210/pdb9KPF/pdb
• EM Map EMD-62486: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, Streptococcus pneumoniae
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2024-11-22 Released: 2025-04-02 
• Deposition Author(s): Wang, X., Wu, L.J., Hua, T., Liu, Z.J.
• Funding Organization(s): Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.15 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Cryo-EM structure of GPCR16-Gi complex

Wang, X., Wu, L.J., Hua, T., Liu, Z.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 232.69 kDa 
• Atom Count: 8,914 
• Modeled Residue Count: 1,127 
• Deposited Residue Count: 2,083 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	369	Homo sapiens	Mutation(s): 0  Gene Names: GNAI1 EC: 3.6.5 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens) Explore P63096  Go to UniProtKB:  P63096
PHAROS:  P63096 GTEx:  ENSG00000127955

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	366	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: 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 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 ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion protein 1,exo-alpha-sialidase,Taste receptor type 2 member 16,Fusion protein 2	D [auth R]	1,011	Homo sapiens, Streptococcus pneumoniae	Mutation(s): 0  EC: 3.2.1.18 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NYV7 (Homo sapiens) Explore Q9NYV7  Go to UniProtKB:  Q9NYV7
PHAROS:  Q9NYV7 GTEx:  ENSG00000128519

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv16	E [auth S]	266	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SA0 (Subject of Investigation/LOI)	F [auth R]	2-(hydroxymethyl)phenyl beta-D-glucopyranoside C13 H18 O7 NGFMICBWJRZIBI-UJPOAAIJSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.15 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-02 
Deposition Author(s): Wang, X., Wu, L.J., Hua, T., Liu, Z.J.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	XDB37030104

Revision History  

• Version 1.0: 2025-04-02
  Type: Initial release