5W0P

Crystal structure of rhodopsin bound to visual arrestin determined by X-ray free electron laser


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.013 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Identification of Phosphorylation Codes for Arrestin Recruitment by G Protein-Coupled Receptors.

Zhou, X.E.He, Y.de Waal, P.W.Gao, X.Kang, Y.Van Eps, N.Yin, Y.Pal, K.Goswami, D.White, T.A.Barty, A.Latorraca, N.R.Chapman, H.N.Hubbell, W.L.Dror, R.O.Stevens, R.C.Cherezov, V.Gurevich, V.V.Griffin, P.R.Ernst, O.P.Melcher, K.Xu, H.E.

(2017) Cell 170: 457-469.e13

  • DOI: 10.1016/j.cell.2017.07.002

  • PubMed Abstract: 
  • G protein-coupled receptors (GPCRs) mediate diverse signaling in part through interaction with arrestins, whose binding promotes receptor internalization and signaling through G protein-independent pathways. High-affinity arrestin binding requires re ...

    G protein-coupled receptors (GPCRs) mediate diverse signaling in part through interaction with arrestins, whose binding promotes receptor internalization and signaling through G protein-independent pathways. High-affinity arrestin binding requires receptor phosphorylation, often at the receptor's C-terminal tail. Here, we report an X-ray free electron laser (XFEL) crystal structure of the rhodopsin-arrestin complex, in which the phosphorylated C terminus of rhodopsin forms an extended intermolecular β sheet with the N-terminal β strands of arrestin. Phosphorylation was detected at rhodopsin C-terminal tail residues T336 and S338. These two phospho-residues, together with E341, form an extensive network of electrostatic interactions with three positively charged pockets in arrestin in a mode that resembles binding of the phosphorylated vasopressin-2 receptor tail to β-arrestin-1. Based on these observations, we derived and validated a set of phosphorylation codes that serve as a common mechanism for phosphorylation-dependent recruitment of arrestins by GPCRs.


    Organizational Affiliation

    Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany; Centre for Ultrafast Imaging, 22761 Hamburg, Germany.,Department of Computer Science, Stanford University, Stanford, CA 94305, USA; Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University, Stanford, CA 94305, USA; Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA; Biophysics Program, Stanford University, Stanford, CA 94305, USA.,Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA.,Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA.,Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA.,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; Laboratory of Structural Sciences, Center for Structural Biology and Drug Discovery, Van Andel Research Institute, Grand Rapids, MI 49503, USA.,Laboratory of Structural Sciences, Center for Structural Biology and Drug Discovery, Van Andel Research Institute, Grand Rapids, MI 49503, USA.,Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany.,Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA.,Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.,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; Laboratory of Structural Sciences, Center for Structural Biology and Drug Discovery, Van Andel Research Institute, Grand Rapids, MI 49503, USA. Electronic address: eric.xu@vai.org.,Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA; iHuman Institute, ShanghaiTech University, 2F Building 6, 99 Haike Road, Pudong New District, Shanghai 201210, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endolysin,Rhodopsin,S-arrestin
A, B
906Homo sapiensMus musculusEnterobacteria phage T4
This entity is chimeric
Mutation(s): 9 
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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Endolysin,Rhodopsin,S-arrestin
C, D
906Homo sapiensMus musculusEnterobacteria phage T4
This entity is chimeric
Mutation(s): 9 
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
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A, B, C, D
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A, B
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.013 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.234 
  • 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
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
PHENIXrefinement

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
Ministry of Science and Technology (China)China2012ZX09301001
Ministry of Science and Technology (China)China2012CB910403
Ministry of Science and Technology (China)China2013CB910600
Ministry of Science and Technology (China)ChinaXDB08020303
Ministry of Science and Technology (China)China2013ZX09507001
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM108635
National Institutes of Health/National Eye InstituteUnited StatesRO1 EY011500
American Asthma FoundationUnited States--
Jay and Betty Van Andel FoundationUnited States--
Canada Excellence Research Chairs programCanada--
Anne and Max Tanenbaum Chair in NeuroscienceCanada--

Revision History 

  • Version 1.0: 2017-08-09
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Author supporting evidence, Data collection
  • Version 1.2: 2018-11-21
    Type: Data collection