5TUD

Structural Insights into the Extracellular Recognition of the Human Serotonin 2B Receptor by an Antibody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history


Literature

Structural insights into the extracellular recognition of the human serotonin 2B receptor by an antibody.

Ishchenko, A.Wacker, D.Kapoor, M.Zhang, A.Han, G.W.Basu, S.Patel, N.Messerschmidt, M.Weierstall, U.Liu, W.Katritch, V.Roth, B.L.Stevens, R.C.Cherezov, V.

(2017) Proc Natl Acad Sci U S A 114: 8223-8228

  • DOI: https://doi.org/10.1073/pnas.1700891114
  • Primary Citation of Related Structures:  
    5TUD

  • PubMed Abstract: 

    Monoclonal antibodies provide an attractive alternative to small-molecule therapies for a wide range of diseases. Given the importance of G protein-coupled receptors (GPCRs) as pharmaceutical targets, there has been an immense interest in developing therapeutic monoclonal antibodies that act on GPCRs. Here we present the 3.0-Å resolution structure of a complex between the human 5-hydroxytryptamine 2B (5-HT 2B ) receptor and an antibody Fab fragment bound to the extracellular side of the receptor, determined by serial femtosecond crystallography with an X-ray free-electron laser. The antibody binds to a 3D epitope of the receptor that includes all three extracellular loops. The 5-HT 2B receptor is captured in a well-defined active-like state, most likely stabilized by the crystal lattice. The structure of the complex sheds light on the mechanism of selectivity in extracellular recognition of GPCRs by monoclonal antibodies.


  • Organizational Affiliation

    Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
5-hydroxytryptamine receptor 2B,Soluble cytochrome b562 chimera
A, D
457Homo sapiensEscherichia coliMutation(s): 4 
Gene Names: HTR2BcybC
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P41595 (Homo sapiens)
Explore P41595 
Go to UniProtKB:  P41595
PHAROS:  P41595
GTEx:  ENSG00000135914 
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0ABE7P41595
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Anti-5-HT2B Fab light chain
B, E
213Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Anti-5-HT2B Fab heavy chain
C, F
236Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.29α = 90
b = 118.86β = 90.37
c = 145.38γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
CrystFELdata reduction
PHASERphasing
CrystFELdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM108635
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM094618

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2017-08-16
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.3: 2018-02-14
    Changes: Data collection
  • Version 1.4: 2018-11-28
    Changes: Data collection
  • Version 1.5: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.6: 2023-10-04
    Changes: Data collection, Database references, Refinement description