5DGY | pdb_00005dgy

Crystal structure of rhodopsin bound to visual arrestin

• PDB DOI: https://doi.org/10.2210/pdb5DGY/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Tequatrovirus T4, Homo sapiens, Mus musculus
• Expression System: Homo sapiens
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2015-08-28 Released: 2016-03-23 
• Deposition Author(s): Zhou, X.E., Gao, X., Kang, Y., He, Y., de Waal, P.W., Suino-Powell, K.M., Wang, M., Melcher, K., Xu, H.E.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Michigan Economic Development Corporation and the Michigan Technology Tri-Corridor

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 7.70 Å
• R-Value Free: 
  0.335 (Depositor), 0.316 (DCC) 
• R-Value Work: 
  0.285 (Depositor), 0.320 (DCC) 
• R-Value Observed: 
  0.288 (Depositor) 

Starting Model: experimental

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

• PubMed: 27070998 
• DOI: https://doi.org/10.1038/sdata.2016.21
• Primary Citation Related Structures: 
  5DGY


• 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), 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.

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Organizational Affiliation: 
• Laboratory of Structural Sciences, Center for Structural Biology and Drug Discovery, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA.
Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany.
School of Molecular Sciences, and Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona 85287-1604, USA.
Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, California 90089, USA.
Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, California 90089, USA.
Joint Center for Structural Genomics, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA.
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 D02 R590, Ireland.
Centre for Ultrafast Imaging, 22761 Hamburg, Germany.
Department of Physics, Arizona State University, Tempe, Arizona 85287, USA.
iHuman Institute, Shanghai Tech University, 2F Building 6, 99 Haike Road, Pudong New District, Shanghai 201210, China.
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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 403.44 kDa 
• Atom Count: 24,665 
• Modeled Residue Count: 3,128 
• Deposited Residue Count: 3,624 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endolysin,Rhodopsin,S-arrestin	A, B, C, D	906	Tequatrovirus T4, Homo sapiens, Mus musculus This entity is chimeric	Mutation(s): 11  EC: 3.2.1.17 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
PHAROS:  P08100 GTEx:  ENSG00000163914
Find proteins for P20443 (Mus musculus) Explore P20443  Go to UniProtKB:  P20443
IMPC:  MGI:98227
UniProt Groups	P00720P08100P20443

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 7.70 Å
• R-Value Free:  0.335 (Depositor), 0.316 (DCC) 
• R-Value Work:  0.285 (Depositor), 0.320 (DCC) 
• R-Value Observed: 0.288 (Depositor) 

Diffraction Data: https://doi.org/10.11577/1241101

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.484	α = 90
b = 107.258	β = 90
c = 460.314	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-03-23 
Deposition Author(s): Zhou, X.E., Gao, X., Kang, Y., He, Y., de Waal, P.W., Suino-Powell, K.M., Wang, M., Melcher, K., Xu, H.E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	DK071662
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	ACB-12002
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	AGM-12006
Michigan Economic Development Corporation and the Michigan Technology Tri-Corridor	United States	085P1000817

Revision History  

• Version 1.0: 2016-03-23
  Type: Initial release
  
• Version 1.1: 2016-04-27
  Changes: Database references
• Version 1.2: 2017-08-09
  Changes: Database references, Derived calculations
• Version 1.3: 2017-09-20
  Changes: Author supporting evidence
• Version 1.4: 2019-12-04
  Changes: Author supporting evidence
• Version 1.5: 2023-08-16
  Changes: Data collection, Database references
• Version 1.6: 2023-09-27
  Changes: Refinement description
• Version 1.7: 2024-10-16
  Changes: Structure summary