5TUD | pdb_00005tud

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

• PDB DOI: https://doi.org/10.2210/pdb5TUD/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, Escherichia coli, Mus musculus
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTM


• Deposited: 2016-11-05 Released: 2017-07-26 
• Deposition Author(s): Ishchenko, A., Wacker, D., Kapoor, M., Zhang, A., Han, G.W., Basu, S., Boutet, S., James, D., Wang, D., Weierstall, U., Liu, W., Katritch, V., Stevens, R.C., Cherezov, V.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.247 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.246 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

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

• PubMed: 28716900 
• DOI: https://doi.org/10.1073/pnas.1700891114
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089.
Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599-7365.
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.
BioXFEL Science and Technology Center, Buffalo, NY 14203.
Department of Physics, Arizona State University, Tempe, AZ 85281.
School of Molecular Sciences, Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287.
Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7365.
National Institute of Mental Health Psychoactive Drug Screening Program, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7365.
Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089; [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 201.43 kDa 
• Atom Count: 12,395 
• Modeled Residue Count: 1,628 
• Deposited Residue Count: 1,812 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-hydroxytryptamine receptor 2B,Soluble cytochrome b562 chimera	A, D	457	Homo sapiens, Escherichia coli	Mutation(s): 4  Gene Names: HTR2B, cybC Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7
Find proteins for P41595 (Homo sapiens) Explore P41595  Go to UniProtKB:  P41595
PHAROS:  P41595 GTEx:  ENSG00000135914
UniProt Groups	P0ABE7P41595

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-5-HT2B Fab light chain	B, E	213	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-5-HT2B Fab heavy chain	C, F	236	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ERM	G [auth A], H [auth D]	Ergotamine C33 H35 N5 O5 XCGSFFUVFURLIX-VFGNJEKYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.247 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.246 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.29	α = 90
b = 118.86	β = 90.37
c = 145.38	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
CrystFEL	data reduction
PHASER	phasing
CrystFEL	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-07-26 
Deposition Author(s): Ishchenko, A., Wacker, D., Kapoor, M., Zhang, A., Han, G.W., Basu, S., Boutet, S., James, D., Wang, D., Weierstall, U., Liu, W., Katritch, V., Stevens, R.C., Cherezov, V.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM108635
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM094618

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
• Version 1.6: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.7: 2024-10-30
  Changes: Structure summary