4ZWJ | pdb_00004zwj

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

• PDB DOI: https://doi.org/10.2210/pdb4ZWJ/pdb

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


• Deposited: 2015-05-19 Released: 2015-07-29 
• Deposition Author(s): 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.E., Zhang, C., Moeller, A., West, G.M., Pascal, B., Eps, N.V., 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., 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.H., 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., GPCR Network (GPCR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.293 (Depositor), 0.291 (DCC) 
• R-Value Work: 
  0.253 (Depositor), 0.252 (DCC) 
• R-Value Observed: 
  0.255 (Depositor) 

Starting Models: experimental

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

• PubMed: 26200343 
• DOI: https://doi.org/10.1038/nature14656
• Primary Citation Related Structures: 
  4ZWJ


• 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.

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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.
Department of Chemistry and Biochemistry, 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.
Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany.
Joint Center for Structural Genomics, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, 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.
The National Resource for Automated Molecular Microscopy, New York Structural Biology Center, New York, New York 10027, USA.
Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter, Florida 33458, USA.
Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA.
Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, USA.
Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California 94025, 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.
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.
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.
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.
State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
Department of Obstetrics &Gynecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
Swiss Light Source at Paul Scherrer Institute, CH-5232 Villigen, Switzerland.
Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, California 90089, USA.
School of Medicine and School of Biochemistry and Immunology, Trinity College, Dublin 2, Ireland.
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.
Laboratory of Biomolecular Research at Paul Scherrer Institute, CH-5232 Villigen, Switzerland.
Department of Biology, Universität Konstanz, 78457 Konstanz, Germany.
Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China.
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 Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada [2] Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
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.
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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

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
Chimera protein of human Rhodopsin, mouse S-arrestin, and T4 Endolysin	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: 3.30 Å
• R-Value Free:  0.293 (Depositor), 0.291 (DCC) 
• R-Value Work:  0.253 (Depositor), 0.252 (DCC) 
• R-Value Observed: 0.255 (Depositor) 

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

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.24	α = 90
b = 109.24	β = 90
c = 452.64	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-29 
Deposition Author(s): 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.E., Zhang, C., Moeller, A., West, G.M., Pascal, B., Eps, N.V., 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., 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.H., 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., GPCR Network (GPCR)

Revision History  

• 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
• Version 1.6: 2024-11-20
  Changes: Structure summary