8ZBE | pdb_00008zbe

cryo-EM structure of the octreotide-bound SSTR5-Gi complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.24 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8ZBE

This is version 1.2 of the entry. See complete history

Literature

Structural insights into somatostatin receptor 5 bound with cyclic peptides.

Li, Y.G.Meng, X.Y.Yang, X.Ling, S.L.Shi, P.Tian, C.L.Yang, F.

(2024) Acta Pharmacol Sin 45: 2432-2440

  • DOI: https://doi.org/10.1038/s41401-024-01314-8
  • Primary Citation Related Structures: 
    8ZBE, 8ZCJ

  • PubMed Abstract: 

    Somatostatin receptor 5 (SSTR5) is highly expressed in ACTH-secreting pituitary adenomas and is an important drug target for the treatment of Cushing's disease. Two cyclic SST analog peptides (pasireotide and octreotide) both can activate SSTR5 and SSTR2. Pasireotide is preferential binding to SSTR5 than octreotide, while octreotide is biased to SSTR2 than SSTR5. The lack of selectivity of both pasireotide and octreotide causes side effects, such as hyperglycemia, gastrointestinal disturbance, and abnormal glucose homeostasis. However, little is known about the binding and selectivity mechanisms of pasireotide and octreotide with SSTR5, limiting the development of subtype-selective SST analog drugs specifically targeting SSTR5. Here, we report two cryo-electron microscopy (cryo-EM) structures of SSTR5-Gi complexes activated by pasireotide and octreoitde at resolutions of 3.09 Å and 3.24 Å, respectively. In combination with structural analysis and functional experiments, our results reveal the molecular mechanisms of ligand recognition and receptor activation. We also demonstrate that pasireotide preferentially binds to SSTR5 through the interactions between Tyr(Bzl)/ D Trp of pasireotide and SSTR5. Moreover, we find that the Q 2.63 , N 6.55 , F 7.35 and ECL2 of SSTR2 play a crucial role in octreotide biased binding of SSTR2. Our results will provide structural insights and offer new opportunities for the drug discovery of better selective pharmaceuticals targeting specific SSTR subtypes.


  • Organizational Affiliation
    • The First Affiliated Hospital of USTC, School of Life Sciences, Division of Life Sciences and Medicine, Joint Center for Biological Analytical Chemistry, Anhui Engineering Laboratory of Peptide Drug, Anhui Laboratory of Advanced Photonic Science and Technology, University of Science and Technology of China, Hefei, 230026, China.

Macromolecule Content 

  • Total Structure Weight: 185.12 kDa 
  • Atom Count: 7,489 
  • Modeled Residue Count: 1,114 
  • Deposited Residue Count: 1,684 
  • Unique protein chains: 6

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2 adrenergic receptor,Somatostatin receptor type 5,lgbit (fusion protein)570Homo sapiensOplophorus gracilirostrisMutation(s): 0 
Gene Names: ADRB2ADRB2RB2ARSSTR5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P07550 (Homo sapiens)
Explore P07550 
Go to UniProtKB:  P07550
PHAROS:  P07550
GTEx:  ENSG00000169252 
Find proteins for P35346 (Homo sapiens)
Explore P35346 
Go to UniProtKB:  P35346
PHAROS:  P35346
GTEx:  ENSG00000162009 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP35346P07550
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1354Homo sapiensMutation(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
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UniProt GroupP63096
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit gammaC [auth D]71Rattus norvegicusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A9X9ZA26 (Rattus norvegicus)
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Go to UniProtKB:  A0A9X9ZA26
Entity Groups
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UniProt GroupA0A9X9ZA26
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
ScFv16D [auth E]304Homo sapiensMutation(s): 0 
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
octreotideE [auth P]8synthetic constructMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1F [auth C]377Rattus norvegicusMutation(s): 0 
Gene Names: Gnb1
UniProt
Find proteins for P54311 (Rattus norvegicus)
Explore P54311 
Go to UniProtKB:  P54311
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UniProt GroupP54311
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.24 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-10
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2024-11-13
    Changes: Data collection