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 

wwPDB Validation   3D Report Full Report


This is version 1.5 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: 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 ...

    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; cherezov@usc.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
5-hydroxytryptamine receptor 2B,Soluble cytochrome b562 chimeraAD457Homo sapiensEscherichia coliMutation(s): 4 
Gene Names: HTR2B
Find proteins for P41595 (Homo sapiens)
Explore P41595 
Go to UniProtKB:  P41595
NIH Common Fund Data Resources
PHAROS  P41595
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Anti-5-HT2B Fab light chainBE213Mus musculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Anti-5-HT2B Fab heavy chainCF236Mus musculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ERM
Query on ERM

Download Ideal Coordinates CCD File 
A, D
Ergotamine
C33 H35 N5 O5
XCGSFFUVFURLIX-VFGNJEKYSA-N
 Ligand Interaction
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

View Full Validation Report



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 

  • 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