8XBH

Human GPR34 -Gi complex bound to M1

• PDB DOI: https://doi.org/10.2210/pdb8XBH/pdb
• EM Map EMD-38218: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Rattus norvegicus, Bos taurus, Mus musculus
• Expression System: unidentified baculovirus
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2023-12-06 Released: 2023-12-27 
• Deposition Author(s): Kawahara, R., Shihoya, W., Nureki, O.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.83 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of the Human GPR34-Gi complex bound to S3E-LysoPS

Nureki, O.

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: 159.82 kDa 
• Atom Count: 8,947 
• Modelled Residue Count: 1,137 
• Deposited Residue Count: 1,422 
• 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	354	Homo sapiens	Mutation(s): 0  Gene Names: GNAI1 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	344	Rattus norvegicus	Mutation(s): 0  Gene Names: Gnb1
UniProt
Find proteins for P54311 (Rattus norvegicus) Explore P54311  Go to UniProtKB:  P54311

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]	68	Bos taurus	Mutation(s): 0  Gene Names: GNG2 Membrane Entity: Yes
UniProt
Find proteins for P63212 (Bos taurus) Explore P63212  Go to UniProtKB:  P63212

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable G-protein coupled receptor 34	D [auth R]	396	Homo sapiens	Mutation(s): 0  Gene Names: GPR34 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UPC5 (Homo sapiens) Explore Q9UPC5  Go to UniProtKB:  Q9UPC5
PHAROS:  Q9UPC5 GTEx:  ENSG00000171659

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv16	E [auth S]	260	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KW3 (Subject of Investigation/LOI)	F [auth R]	(2~{S})-2-azanyl-3-[[(2~{R})-1-ethoxy-3-[3-[2-[(3-phenoxyphenyl)methoxy]phenyl]propanoyloxy]propan-2-yl]oxy-oxidanyl-phosphoryl]oxy-propanoic acid C30 H36 N O11 P PWIBLZZVGUIXAU-SXOMAYOGSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.83 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-27 
Deposition Author(s): Kawahara, R., Shihoya, W., Nureki, O.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	21H05037

Revision History  

• Version 1.0: 2023-12-27
  Type: Initial release