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 

wwPDB Validation 3D Report Full Report



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: 10.1038/s41598-020-68355-x
  • Structures With Same Primary Citation

  • 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 ver ...

    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., Shizuoka, Japan. jun.saito.su@kyowakirin.com.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IGG LIGHT CHAINL214Mus musculusMutation(s): 0 
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IGG HEAVY CHAINH323Mus musculusMutation(s): 0 
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
5-hydroxytryptamine receptor 1B,Soluble cytochrome b562,5-hydroxytryptamine receptor 1BA399Homo sapiensEscherichia coliMutation(s): 4 
Gene Names: HTR1BHTR1DB
Find proteins for P28222 (Homo sapiens)
Explore P28222 
Go to UniProtKB:  P28222
NIH Common Fund Data Resources
PHAROS  P28222
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ERM
Query on ERM

Download CCD File 
A
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: 0.290 
  • 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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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-07-29
    Type: Initial release