8ZBI | pdb_00008zbi

Cryo-EM structure of Somatostatin receptor 3 (SSTR3) with Gi1 complex

• PDB DOI: https://doi.org/10.2210/pdb8ZBI/pdb
• EM Map EMD-39902: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda, synthetic construct
• Mutation(s): No 
• Membrane Protein: Yes  MemProtMD


• Deposited: 2024-04-26 Released: 2025-04-30 
• Deposition Author(s): Yun, J.H.
• Funding Organization(s): Institute for Basic Science

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.79 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

The structures of SSTR3 and SSTR5 provide insights into the specificity among somatostatin receptors

Heo, Y., Kim, Y., Cho, M., Kim, C., Ryu, B., Kang, H.J., Lee, W., Yun, J.H.

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: gel filtration

Macromolecule Content 

• Total Structure Weight: 176.92 kDa 
• Atom Count: 7,657 
• Modeled Residue Count: 984 
• Deposited Residue Count: 1,604 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1	A [auth B]	354	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 [auth C]	345	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 E]	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
scFv16	D [auth F]	296	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562,Somatostatin receptor type 3	E [auth D]	524	Homo sapiens	Mutation(s): 0  Gene Names: cybC, SSTR3 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P32745 (Homo sapiens) Explore P32745  Go to UniProtKB:  P32745
PHAROS:  P32745 GTEx:  ENSG00000278195

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Somatostatin-14	F [auth S]	14	Homo sapiens	Mutation(s): 0  Gene Names: SST Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P61278 (Homo sapiens) Explore P61278  Go to UniProtKB:  P61278
PHAROS:  P61278 GTEx:  ENSG00000157005

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 6
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001216	F [auth S]	Somatostatin-14	Cyclic peptide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.79 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX	1.19.2

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-30 
Deposition Author(s): Yun, J.H.

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Funding Organization	Location	Grant Number
Institute for Basic Science	Korea, Republic Of	IBS-R021-D1-2023-a00
Institute for Basic Science	Korea, Republic Of	IBS-R021-D1-2024-a00

Revision History  

• Version 1.0: 2025-04-30
  Type: Initial release