7UL3

CryoEM Structure of Inactive H2R Bound to Famotidine, Nb6M, and NabFab


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structure determination of inactive-state GPCRs with a universal nanobody.

Robertson, M.J.Papasergi-Scott, M.M.He, F.Seven, A.B.Meyerowitz, J.G.Panova, O.Peroto, M.C.Che, T.Skiniotis, G.

(2022) Nat Struct Mol Biol 29: 1188-1195

  • DOI: https://doi.org/10.1038/s41594-022-00859-8
  • Primary Citation of Related Structures:  
    7UL2, 7UL3, 7UL4, 7UL5

  • PubMed Abstract: 

    Cryogenic electron microscopy (cryo-EM) has widened the field of structure-based drug discovery by allowing for routine determination of membrane protein structures previously intractable. Despite representing one of the largest classes of therapeutic targets, most inactive-state G protein-coupled receptors (GPCRs) have remained inaccessible for cryo-EM because their small size and membrane-embedded nature impedes projection alignment for high-resolution map reconstructions. Here we demonstrate that the same single-chain camelid antibody (nanobody) recognizing a grafted intracellular loop can be used to obtain cryo-EM structures of inactive-state GPCRs at resolutions comparable or better than those obtained by X-ray crystallography. Using this approach, we obtained structures of neurotensin 1 receptor bound to antagonist SR48692, μ-opioid receptor bound to alvimopan, apo somatostatin receptor 2 and histamine receptor 2 bound to famotidine. We expect this rapid, straightforward approach to facilitate the broad exploration of GPCR inactive states without the need for extensive engineering and crystallization.


  • Organizational Affiliation

    Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histamine H2 receptor400Homo sapiensMutation(s): 0 
Gene Names: HRH2OPRK1
UniProt & NIH Common Fund Data Resources
Find proteins for P25021 (Homo sapiens)
Go to UniProtKB:  P25021
PHAROS:  P25021
GTEx:  ENSG00000113749 
Find proteins for P41145 (Homo sapiens)
Go to UniProtKB:  P41145
PHAROS:  P41145
GTEx:  ENSG00000082556 
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody 6MB [auth C]131synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NabFab HCC [auth H]239synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NabFab LCD [auth L]215synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FO9 (Subject of Investigation/LOI)
Query on FO9

Download Ideal Coordinates CCD File 
E [auth A]famotidine
C8 H17 N7 O2 S3
YFGRAZUYIUBWJO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The G. Harold and Leila Y. Mathers FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-29
    Type: Initial release
  • Version 1.1: 2022-11-23
    Changes: Database references
  • Version 1.2: 2022-11-30
    Changes: Database references
  • Version 1.3: 2022-12-28
    Changes: Database references
  • Version 1.4: 2024-09-25
    Changes: Data collection, Source and taxonomy
  • Version 1.5: 2024-10-09
    Changes: Data collection, Structure summary