Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser

Experimental Data Snapshot

  • Resolution: 3.30 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.255 

wwPDB Validation   3D Report Full Report

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Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser.

Kang, Y.Zhou, X.E.Gao, X.He, Y.Liu, W.Ishchenko, A.Barty, A.White, T.A.Yefanov, O.Han, G.W.Xu, Q.de Waal, P.W.Ke, J.Tan, M.H.Zhang, C.Moeller, A.West, G.M.Pascal, B.D.Van Eps, N.Caro, L.N.Vishnivetskiy, S.A.Lee, R.J.Suino-Powell, K.M.Gu, X.Pal, K.Ma, J.Zhi, X.Boutet, S.Williams, G.J.Messerschmidt, M.Gati, C.Zatsepin, N.A.Wang, D.James, D.Basu, S.Roy-Chowdhury, S.Conrad, C.E.Coe, J.Liu, H.Lisova, S.Kupitz, C.Grotjohann, I.Fromme, R.Jiang, Y.Tan, M.Yang, H.Li, J.Wang, M.Zheng, Z.Li, D.Howe, N.Zhao, Y.Standfuss, J.Diederichs, K.Dong, Y.Potter, C.S.Carragher, B.Caffrey, M.Jiang, H.Chapman, H.N.Spence, J.C.Fromme, P.Weierstall, U.Ernst, O.P.Katritch, V.Gurevich, V.V.Griffin, P.R.Hubbell, W.L.Stevens, R.C.Cherezov, V.Melcher, K.Xu, H.E.

(2015) Nature 523: 561-567

  • DOI: https://doi.org/10.1038/nature14656
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    G-protein-coupled receptors (GPCRs) signal primarily through G proteins or arrestins. Arrestin binding to GPCRs blocks G protein interaction and redirects signalling to numerous G-protein-independent pathways. Here we report the crystal structure of a constitutively active form of human rhodopsin bound to a pre-activated form of the mouse visual arrestin, determined by serial femtosecond X-ray laser crystallography. Together with extensive biochemical and mutagenesis data, the structure reveals an overall architecture of the rhodopsin-arrestin assembly in which rhodopsin uses distinct structural elements, including transmembrane helix 7 and helix 8, to recruit arrestin. Correspondingly, arrestin adopts the pre-activated conformation, with a ∼20° rotation between the amino and carboxy domains, which opens up a cleft in arrestin to accommodate a short helix formed by the second intracellular loop of rhodopsin. This structure provides a basis for understanding GPCR-mediated arrestin-biased signalling and demonstrates the power of X-ray lasers for advancing the frontiers of structural biology.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chimera protein of human Rhodopsin, mouse S-arrestin, and T4 Endolysin
A, B, C, D
906Tequatrovirus T4Homo sapiensMus musculus
This entity is chimeric
Mutation(s): 11 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Find proteins for P08100 (Homo sapiens)
Explore P08100 
Go to UniProtKB:  P08100
GTEx:  ENSG00000163914 
Find proteins for P20443 (Mus musculus)
Explore P20443 
Go to UniProtKB:  P20443
IMPC:  MGI:98227
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP00720P08100P20443
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.24α = 90
b = 109.24β = 90
c = 452.64γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
CrystFELdata reduction
CrystFELdata scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-29
    Type: Initial release
  • Version 1.1: 2015-08-05
    Changes: Database references
  • Version 1.2: 2015-08-12
    Changes: Database references
  • Version 1.3: 2018-02-14
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2023-08-16
    Changes: Data collection, Database references
  • Version 1.5: 2023-09-27
    Changes: Refinement description