4ZWJ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.302 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.253 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 10.1038/nature14656

  • 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 ...

    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.,Department of Biology, Universität Konstanz, 78457 Konstanz, Germany.,Laboratory of Biomolecular Research at Paul Scherrer Institute, CH-5232 Villigen, Switzerland.,Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter, Florida 33458, USA.,1] Department of Chemistry and Biochemistry, and Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona 85287-1604, USA [2] Beijing Computational Science Research Center, Haidian District, Beijing 10084, China.,Department of Chemistry and Biochemistry, and Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona 85287-1604, USA.,The National Resource for Automated Molecular Microscopy, New York Structural Biology Center, New York, New York 10027, USA.,1] Laboratory of Structural Sciences, Center for Structural Biology and Drug Discovery, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA [2] VARI-SIMM Center, Center for Structure and Function of Drug Targets, CAS-Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, USA.,1] Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada [2] Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany.,Department of Obstetrics &Gynecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,1] BioXFEL, NSF Science and Technology Center, 700 Ellicott Street, Buffalo, New York 14203, USA [2] Ben May Department for Cancer Research, University of Chicago, Chicago, Illinois 60637, USA.,1] Laboratory of Structural Sciences, Center for Structural Biology and Drug Discovery, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA [2] Department of Obstetrics &Gynecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,1] Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany [2] Centre for Ultrafast Imaging, 22761 Hamburg, Germany.,1] Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, California 90089, USA [2] Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, California 90089, USA [3] iHuman Institute, ShanghaiTech University, 2F Building 6, 99 Haike Road, Pudong New District, Shanghai 201210, China.,Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, California 90089, USA.,1] Department of Chemistry and Biochemistry, and Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona 85287-1604, USA [2] Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, USA.,1] Department of Chemistry and Biochemistry, and Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona 85287-1604, USA [2] Department of Physics, Arizona State University, Tempe, Arizona 85287, USA.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA.,Swiss Light Source at Paul Scherrer Institute, CH-5232 Villigen, Switzerland.,School of Medicine and School of Biochemistry and Immunology, Trinity College, Dublin 2, Ireland.,Joint Center for Structural Genomics, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA.,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA.,1] Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA [2] BioXFEL, NSF Science and Technology Center, 700 Ellicott Street, Buffalo, New York 14203, USA.,Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, California 90089, USA.,Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chimera protein of human Rhodopsin, mouse S-arrestin, and T4 Endolysin
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
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
Human rhodopsin with bound mouse visual arrestin
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: 3.302 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.253 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 109.240α = 90.00
b = 109.240β = 90.00
c = 452.640γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
PHENIXrefinement
CrystFELdata scaling
CrystFELdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History