Biological Assembly 1  

 3D View: Structure | Electron Density

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

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

Biological Assembly 2  

 3D View: Structure | Electron Density

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

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

Biological Assembly 3  

 3D View: Structure | Electron Density

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

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

Biological Assembly 4  

 3D View: Structure | Electron Density

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: 24665 
• Modelled Residue Count: 3128 
• Deposited Residue Count: 3624 
• Unique protein chains: 1

4ZWJ

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

• DOI: 10.2210/pdb4ZWJ/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Escherichia virus T4, Homo sapiens, Mus musculus
• Expression System: Homo sapiens
• Mutation(s): Yes 


• 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 
• R-Value Work: 0.253 
• R-Value Observed: 0.255 

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: 10.1038/nature14656
• Primary Citation of 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: 

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.

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	Escherichia virus T4, Homo sapiens, Mus musculus This entity is chimeric	Mutation(s): 11  Gene Names: E, RHO, OPN2, Sag EC: 3.2.1.17
Membrane protein Mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  G Protein-Coupled Receptors: Class A	Protein:  Human rhodopsin with bound mouse visual arrestin
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
NIH Common Fund Data Resources
PHAROS:  P08100 GTEx:  ENSG00000163914
Find proteins for P20443 (Mus musculus) Explore P20443  Go to UniProtKB:  P20443
NIH Common Fund Data Resources
IMPC:  MGI:98227

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.293 
• R-Value Work: 0.253 
• R-Value Observed: 0.255 
• 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

• Deposited Date: 2015-05-19 
• 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