7C61

Crystal structure of 5-HT1B-BRIL and SRP2070_Fab complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.254 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

The discovery of a new antibody for BRIL-fused GPCR structure determination.

Miyagi, H.Asada, H.Suzuki, M.Takahashi, Y.Yasunaga, M.Suno, C.Iwata, S.Saito, J.I.

(2020) Sci Rep 10: 11669-11669

  • DOI: https://doi.org/10.1038/s41598-020-68355-x
  • Primary Citation of Related Structures:  
    7C61, 7C6A

  • PubMed Abstract: 

    G-protein-coupled receptors (GPCRs)-the largest family of cell-surface membrane proteins-mediate the intracellular signal transduction of many external ligands. Thus, GPCRs have become important drug targets. X-ray crystal structures of GPCRs are very useful for structure-based drug design (SBDD). Herein, we produced a new antibody (SRP2070) targeting the thermostabilised apocytochrome b562 from Escherichia coli M7W/H102I/R106L (BRIL). We found that a fragment of this antibody (SRP2070Fab) facilitated the crystallisation of the BRIL-tagged, ligand bound GPCRs, 5HT 1B and AT 2 R. Furthermore, the electron densities of the ligands were resolved, suggesting that SPR2070Fab is versatile and adaptable for GPCR SBDD. We anticipate that this new tool will significantly accelerate structure determination of other GPCRs and the design of small molecular drugs targeting them.


  • Organizational Affiliation

    R&D Division, Kyowa Kirin Co., Ltd., Tokyo, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IGG LIGHT CHAINA [auth L]214Mus musculusMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
IGG HEAVY CHAINB [auth H]323Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
5-hydroxytryptamine receptor 1B,Soluble cytochrome b562,5-hydroxytryptamine receptor 1BC [auth A]399Homo sapiensEscherichia coliMutation(s): 4 
Gene Names: HTR1BHTR1DBcybC
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P28222 (Homo sapiens)
Explore P28222 
Go to UniProtKB:  P28222
PHAROS:  P28222
GTEx:  ENSG00000135312 
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP28222P0ABE7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ERM (Subject of Investigation/LOI)
Query on ERM

Download Ideal Coordinates CCD File 
D [auth A]Ergotamine
C33 H35 N5 O5
XCGSFFUVFURLIX-VFGNJEKYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.254 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 248.8α = 90
b = 65.7β = 98.79
c = 79.73γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-29
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Refinement description