7WIC | pdb_00007wic

Cryo-EM structure of the SS-14-bound human SSTR2-Gi1 complex

• PDB DOI: https://doi.org/10.2210/pdb7WIC/pdb
• EM Map EMD-32528: EMDB EMDataResource

• Classification: STRUCTURAL PROTEIN
• Organism(s): Homo sapiens, Rattus norvegicus, Bos taurus, synthetic construct
• Expression System: Spodoptera frugiperda, Trichoplusia ni
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMmpstruc


• Deposited: 2022-01-03 Released: 2022-06-01 
• Deposition Author(s): Chen, L., Wang, W., Dong, Y., Shen, D., Guo, J., Qin, J., Zhang, H., Shen, Q., Zhang, Y., Mao, C.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Structures of the endogenous peptide- and selective non-peptide agonist-bound SSTR2 signaling complexes.

Chen, L.N., Wang, W.W., Dong, Y.J., Shen, D.D., Guo, J., Yu, X., Qin, J., Ji, S.Y., Zhang, H., Shen, Q., He, Q., Yang, B., Zhang, Y., Li, Q., Mao, C.

(2022) Cell Res 32: 785-788

• PubMed: 35578016 
• DOI: https://doi.org/10.1038/s41422-022-00669-z
• Primary Citation of Related Structures:  
  7WIC, 7WIG

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Organizational Affiliation: 
• Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University, School of Medicine, Hangzhou, Zhejiang, China.
Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
Center for Structural Pharmacology and Therapeutics Development, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang, China.
The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, China.
Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
Zhejiang Provincial Key Laboratory of Immunity and Inflammatory diseases, Hangzhou, Zhejiang, China.
The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, China. [e-mail].
Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China. [e-mail].
Center for Structural Pharmacology and Therapeutics Development, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 157.88 kDa 
• Atom Count: 9,048 
• Modeled Residue Count: 1,158 
• Deposited Residue Count: 1,421 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
somatostatin-14	A [auth L]	14	Homo sapiens	Mutation(s): 0  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Somatostatin receptor type 2	B [auth R]	369	Homo sapiens	Mutation(s): 0  Gene Names: SSTR2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P30874 (Homo sapiens) Explore P30874  Go to UniProtKB:  P30874
PHAROS:  P30874 GTEx:  ENSG00000180616

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1	C [auth A]	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	D [auth B]	345	Rattus norvegicus	Mutation(s): 0  Gene Names: Gnb1
UniProt
Find proteins for P54311 (Rattus norvegicus) Explore P54311  Go to UniProtKB:  P54311

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]	70	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: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
single Fab chain (svFv16)	F [auth S]	269	synthetic construct	Mutation(s): 0

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001216	A [auth L]	Somatostatin-14	Cyclic peptide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0
MODEL REFINEMENT	PHENIX	1.16

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-01 
Deposition Author(s): Chen, L., Wang, W., Dong, Y., Shen, D., Guo, J., Qin, J., Zhang, H., Shen, Q., Zhang, Y., Mao, C.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-06-01
  Type: Initial release
  
• Version 1.1: 2022-08-17
  Changes: Database references
• Version 1.2: 2024-11-13
  Changes: Data collection, Refinement description, Structure summary