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 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.4 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

  • 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.,Department of Integrative Structural, and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037.,Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85281.,Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089.,Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089; cherezov@usc.edu.,BioXFEL Science and Technology Center, Buffalo, NY 14203.,Department of Physics, Arizona State University, Tempe, AZ 85281.,Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7365.,Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599-7365.,School of Molecular Sciences, Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287.,National Institute of Mental Health Psychoactive Drug Screening Program, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7365.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5-hydroxytryptamine receptor 2B,Soluble cytochrome b562 chimera
A, D
457Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 4 
Gene Names: cybC, HTR2B
Find proteins for P0ABE7 (Escherichia coli)
Go to UniProtKB:  P0ABE7
Find proteins for P41595 (Homo sapiens)
Go to Gene View: HTR2B
Go to UniProtKB:  P41595
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Anti-5-HT2B Fab light chain
B, E
213N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Anti-5-HT2B Fab heavy chain
C, F
236N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ERM
Query on ERM

Download SDF File 
Download 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 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.227 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 71.290α = 90.00
b = 118.860β = 90.37
c = 145.380γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
PHASERphasing
CrystFELdata reduction
CrystFELdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM108635
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM094618

Revision History 

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2017-08-16
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence
  • Version 1.3: 2018-02-14
    Type: Data collection
  • Version 1.4: 2018-11-28
    Type: Data collection