5DGY

Crystal structure of rhodopsin bound to visual arrestin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.7 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.285 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex.

Zhou, X.E.Gao, X.Barty, A.Kang, Y.He, Y.Liu, W.Ishchenko, A.White, T.A.Yefanov, O.Han, G.W.Xu, Q.de Waal, P.W.Suino-Powell, K.M.Boutet, S.Williams, G.J.Wang, M.Li, D.Caffrey, M.Chapman, H.N.Spence, J.C.Fromme, P.Weierstall, U.Stevens, R.C.Cherezov, V.Melcher, K.Xu, H.E.

(2016) Sci Data 3: 160021-160021

  • DOI: 10.1038/sdata.2016.21

  • PubMed Abstract: 
  • Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), whi ...

    Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.


    Organizational Affiliation

    Laboratory of Structural Sciences, Center for Structural Biology and Drug Discovery, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endolysin,Rhodopsin,S-arrestin
A, B, C, D
906Homo sapiensMus musculusEnterobacteria phage T4
This entity is chimeric
Mutation(s): 11 
Gene Names: RHO (OPN2), Sag, E
EC: 3.2.1.17
Find proteins for P08100 (Homo sapiens)
Go to Gene View: RHO
Go to UniProtKB:  P08100
Find proteins for P20443 (Mus musculus)
Go to UniProtKB:  P20443
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.7 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.285 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 107.484α = 90.00
b = 107.258β = 90.00
c = 460.314γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata 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 Diabetes and Digestive and Kidney DiseaseUnited StatesDK071662
National Institutes of Health/National Cancer InstituteUnited StatesACB-12002
National Institutes of Health/National Institute of General Medical SciencesUnited StatesAGM-12006
Michigan Economic Development Corporation and the Michigan Technology Tri-CorridorUnited States085P1000817

Revision History 

  • Version 1.0: 2016-03-23
    Type: Initial release
  • Version 1.1: 2016-04-27
    Type: Database references
  • Version 1.2: 2017-08-09
    Type: Database references, Derived calculations
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence