8IZ4 | pdb_00008iz4

Lysophosphatidylserine receptor GPR34-Gi complex

• PDB DOI: https://doi.org/10.2210/pdb8IZ4/pdb
• EM Map EMD-35833: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Spodoptera frugiperda, Trichoplusia ni
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTM


• Deposited: 2023-04-06 Released: 2024-04-10 
• Deposition Author(s): Gong, W., Liu, G., Li, X., Zhang, X.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.93 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural mechanisms of ligand binding and signaling in lysophosphatidylserine receptors

Gong, W., Liu, G., Li, X., Wang, Y., Zhang, X.

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: 182.21 kDa 
• Atom Count: 8,857 
• Modeled Residue Count: 1,134 
• Deposited Residue Count: 1,628 
• 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): 4  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	376	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	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
Antibody fragment scFv16	D [auth E]	255	synthetic construct	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable G-protein coupled receptor 34	E [auth R]	572	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TJR (Subject of Investigation/LOI)	F [auth R]	[(2~{R})-2-oxidanyl-3-phosphonooxy-propyl] octadecanoate C21 H43 O7 P LAYXSTYJRSVXIH-HXUWFJFHSA-N
CLR	H [auth R]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
SER	G [auth R]	SERINE C3 H7 N O3 MTCFGRXMJLQNBG-REOHCLBHSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.93 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: 2024-04-10 
Deposition Author(s): Gong, W., Liu, G., Li, X., Zhang, X.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-04-10
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Structure summary