7YAE | pdb_00007yae

Octreotide-bound SSTR2-Gi complex

PDB DOI: https://doi.org/10.2210/pdb7YAE/pdb
EM Map EMD-33710: EMDB EMDataResource

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens, Mus musculus, synthetic construct
Expression System: Spodoptera frugiperda
Mutation(s): No
Membrane Protein: Yes OPM PDBTM mpstruc

Deposited: 2022-06-28 Released: 2023-04-19
Deposition Author(s): Zhao, J., Shao, Z.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.37 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Prospect of acromegaly therapy: molecular mechanism of clinical drugs octreotide and paltusotine.

Zhao, J., Fu, H., Yu, J., Hong, W., Tian, X., Qi, J., Sun, S., Zhao, C., Wu, C., Xu, Z., Cheng, L., Chai, R., Yan, W., Wei, X., Shao, Z.

(2023) Nat Commun 14: 962-962

PubMed: 36810324 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-023-36673-z
Primary Citation Related Structures:
7YAC, 7YAE

PubMed Abstract:
Somatostatin receptor 2 (SSTR2) is highly expressed in neuroendocrine tumors and represents as a therapeutic target. Several peptide analogs mimicking the endogenous ligand somatostatin are available for clinical use, but poor therapeutic effects occur in a subset of patients, which may be correlated with subtype selectivity or cell surface expression. Here, we clarify the signal bias profiles of the first-generation peptide drug octreotide and a new-generation small molecule paltusotine by evaluating their pharmacological characteristics. We then perform cryo-electron microscopy analysis of SSTR2-Gi complexes to determine how the drugs activate SSTR2 in a selective manner. In this work, we decipher the mechanism of ligand recognition, subtype selectivity and signal bias property of SSTR2 sensing octreotide and paltusotine, which may aid in designing therapeutic drugs with specific pharmacological profiles against neuroendocrine tumors.

Organizational Affiliation

Division of Nephrology and Kidney Research Institute, Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.

State Key Laboratory of Bioelectronics, Department of Otolaryngology Head and Neck Surgery, Zhongda Hospital, School of Life Sciences and Technology, Advanced Institute for Life and Health, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, Southeast University, Nanjing, 210096, China.

Department of Otolaryngology Head and Neck Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China.

Department of Otolaryngology Head and Neck Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China. renjiec@seu.edu.cn.

Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China. renjiec@seu.edu.cn.

Division of Nephrology and Kidney Research Institute, Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China. weiyan2018@scu.edu.cn.

Department of Nephrology, Hainan General Hospital, Haikou, Hainan, 570311, China. zhenhuashao@scu.edu.cn.

Macromolecule Content

Total Structure Weight: 158.7 kDa
Atom Count: 9,031
Modeled Residue Count: 1,148
Deposited Residue Count: 1,419
Unique protein chains: 6

Macromolecules

Find similar proteins by:

| 3D Structure

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 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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63096
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	350	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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62873
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P59768
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv16	D [auth S]	259	Mus musculus	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Somatostatin receptor type 2	E	377	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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P30874
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DPN-CYS-PHE-DTR-LYS-THR-CYS-THO	F [auth D]	8	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLR Query on CLR Download:Ideal Coordinates CCD File SDF format, chain H [auth E] SDF format, chain G [auth E] MOL2 format, chain H [auth E] MOL2 format, chain G [auth E] mmCIF format, chain H [auth E] mmCIF format, chain G [auth E]	G [auth E], H [auth E]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain G [auth E] Focus chain H [auth E] Interactions & Density Focus chain G [auth E] Focus chain H [auth E]