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- PDB-4zwj: Crystal structure of rhodopsin bound to arrestin by femtosecond X... -

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Entry
Database: PDB / ID: 4zwj
TitleCrystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser
ComponentsChimera protein of human Rhodopsin, mouse S-arrestin, and T4 Endolysin
KeywordsSIGNALING PROTEIN / GPCR / rhodopsin / visual arrestin / X-ray free electron laser / serial femtosecond crystallography / Structural Genomics / GPCR Network
Function / homology
Function and homology information


Opsins / Inactivation, recovery and regulation of the phototransduction cascade / rod photoreceptor outer segment / rod bipolar cell differentiation / sperm head plasma membrane / podosome assembly / absorption of visible light / opsin binding / : / G protein-coupled photoreceptor activity ...Opsins / Inactivation, recovery and regulation of the phototransduction cascade / rod photoreceptor outer segment / rod bipolar cell differentiation / sperm head plasma membrane / podosome assembly / absorption of visible light / opsin binding / : / G protein-coupled photoreceptor activity / photoreceptor inner segment membrane / rhodopsin mediated signaling pathway / VxPx cargo-targeting to cilium / 11-cis retinal binding / cellular response to light stimulus / Golgi-associated vesicle membrane / phototransduction, visible light / thermotaxis / detection of temperature stimulus involved in thermoception / photoreceptor cell maintenance / G protein-coupled receptor internalization / ciliary membrane / photoreceptor outer segment membrane / spectrin binding / The canonical retinoid cycle in rods (twilight vision) / phototransduction / photoreceptor outer segment / viral release from host cell by cytolysis / sperm midpiece / photoreceptor inner segment / visual perception / peptidoglycan catabolic process / G protein-coupled receptor binding / G protein-coupled receptor activity / phosphoprotein binding / Activation of the phototransduction cascade / microtubule cytoskeleton organization / photoreceptor disc membrane / Inactivation, recovery and regulation of the phototransduction cascade / cell-cell junction / cell wall macromolecule catabolic process / lysozyme / gene expression / lysozyme activity / G alpha (i) signalling events / host cell cytoplasm / defense response to bacterium / G protein-coupled receptor signaling pathway / Golgi membrane / Golgi apparatus / signal transduction / membrane / metal ion binding / plasma membrane
Similarity search - Function
Rhodopsin, N-terminal / Amino terminal of the G-protein receptor rhodopsin / Rhodopsin / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. ...Rhodopsin, N-terminal / Amino terminal of the G-protein receptor rhodopsin / Rhodopsin / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin-like, C-terminal / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Lysozyme-like domain superfamily / Immunoglobulin E-set
Similarity search - Domain/homology
Endolysin / Rhodopsin / S-arrestin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Homo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 3.302 Å
AuthorsKang, Y. / Zhou, X.E. / Gao, X. / He, Y. / Liu, W. / Ishchenko, A. / Barty, A. / White, T.A. / Yefanov, O. / Han, G.W. ...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)
CitationJournal: Nature / Year: 2015
Title: Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser.
Authors: 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. ...Authors: 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.
History
DepositionMay 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Aug 12, 2015Group: Database references
Revision 1.3Feb 14, 2018Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_beamline ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Sep 27, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chimera protein of human Rhodopsin, mouse S-arrestin, and T4 Endolysin
B: Chimera protein of human Rhodopsin, mouse S-arrestin, and T4 Endolysin
C: Chimera protein of human Rhodopsin, mouse S-arrestin, and T4 Endolysin
D: Chimera protein of human Rhodopsin, mouse S-arrestin, and T4 Endolysin


Theoretical massNumber of molelcules
Total (without water)403,4444
Polymers403,4444
Non-polymers00
Water0
1
A: Chimera protein of human Rhodopsin, mouse S-arrestin, and T4 Endolysin


Theoretical massNumber of molelcules
Total (without water)100,8611
Polymers100,8611
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chimera protein of human Rhodopsin, mouse S-arrestin, and T4 Endolysin


Theoretical massNumber of molelcules
Total (without water)100,8611
Polymers100,8611
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Chimera protein of human Rhodopsin, mouse S-arrestin, and T4 Endolysin


Theoretical massNumber of molelcules
Total (without water)100,8611
Polymers100,8611
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Chimera protein of human Rhodopsin, mouse S-arrestin, and T4 Endolysin


Theoretical massNumber of molelcules
Total (without water)100,8611
Polymers100,8611
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.240, 109.240, 452.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Chimera protein of human Rhodopsin, mouse S-arrestin, and T4 Endolysin / / Lysis protein / Lysozyme / Muramidase / Opsin-2 / 48 kDa protein / Retinal S-antigen / S-AG / Rod ...Lysis protein / Lysozyme / Muramidase / Opsin-2 / 48 kDa protein / Retinal S-antigen / S-AG / Rod photoreceptor arrestin


Mass: 100861.102 Da / Num. of mol.: 4
Mutation: R12G, C54T, C97A , I137R,N2C, E113Q, M257Y, N282C,L374A, V375A, F376A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Homo sapiens (human), (gene. exp.) Mus musculus (house mouse)
Cell line: HEK293S / Gene: RHO, OPN2, Sag / Cell line (production host): HEK293S / Production host: Homo sapiens (human)
References: UniProt: P00720, UniProt: P08100, UniProt: P20443, lysozyme

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.38 Å3/Da / Density % sol: 63.64 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5 / Details: PEG400, sodium acetate, magnesium acetate / PH range: 5.0-6.0

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.32 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Nov 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.32 Å / Relative weight: 1
Reflection twinOperator: k,h,-l / Fraction: 0.5
ReflectionResolution: 3.3→31.5 Å / Num. all: 62613 / Num. obs: 62613 / % possible obs: 76.3 % / Redundancy: 383.3 % / Biso Wilson estimate: 112 Å2 / Rsym value: 0.19 / Net I/σ(I): 4.7
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 116.4 % / % possible all: 6.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4A4M, 4J2Q, 3SN6

4a4m

4j2q

3sn6


Resolution: 3.302→31.038 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.47 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.293 3098 4.95 %Random selection
Rwork0.2525 ---
obs0.2552 62613 76.07 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.302→31.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24665 0 0 0 24665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00825275
X-RAY DIFFRACTIONf_angle_d1.02134346
X-RAY DIFFRACTIONf_dihedral_angle_d11.1559185
X-RAY DIFFRACTIONf_chiral_restr0.0453942
X-RAY DIFFRACTIONf_plane_restr0.0084322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3144-3.37150.3987100.3314165X-RAY DIFFRACTION4
3.3715-3.43270.4129180.3101407X-RAY DIFFRACTION10
3.4327-3.49860.3226460.2787676X-RAY DIFFRACTION17
3.4986-3.56980.3342540.3132991X-RAY DIFFRACTION25
3.5698-3.64730.3747610.31551449X-RAY DIFFRACTION36
3.6473-3.73190.43141080.33571994X-RAY DIFFRACTION50
3.7319-3.8250.34151310.32833127X-RAY DIFFRACTION78
3.825-3.92810.3062190.32843862X-RAY DIFFRACTION95
3.9281-4.04340.31382020.30163829X-RAY DIFFRACTION95
4.0434-4.17340.29162120.29533807X-RAY DIFFRACTION95
4.1734-4.32210.31341900.273847X-RAY DIFFRACTION95
4.3221-4.49440.34222150.26153825X-RAY DIFFRACTION95
4.4944-4.6980.29042160.23923882X-RAY DIFFRACTION95
4.698-4.94430.30232190.23323844X-RAY DIFFRACTION95
4.9443-5.2520.25871770.22923884X-RAY DIFFRACTION96
5.252-5.65420.32811930.26533890X-RAY DIFFRACTION95
5.6542-6.21720.34732060.26953914X-RAY DIFFRACTION95
6.2172-7.10310.26351970.24713918X-RAY DIFFRACTION95
7.1031-8.89790.24722210.21363971X-RAY DIFFRACTION95
8.8979-27.38750.26232030.21764173X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.53770.0856-1.16473.1154-0.06762.96460.03471.0702-0.23260.09190.0981-0.60930.3241-0.4654-0.13280.9082-0.08730.06981.14130.01311.6461-43.6841-63.8356111.5349
24.3596-0.7358-0.73782.38961.12961.57650.3165-0.0503-0.07260.0481-0.2777-0.3055-0.07890.1114-0.03880.7723-0.53690.06281.0725-0.07551.61067.1015-6.1828111.6922
35.27790.0094-0.10194.52271.2641.8171-0.0028-0.24230.57760.64390.2319-0.3494-0.5381-0.5699-0.22911.38520.1256-0.08580.66330.02940.9386-33.8911-16.4789227.5253
44.3825-1.6535-1.59465.6950.27320.6591-0.2184-0.47060.19250.99360.32230.2880.03990.1875-0.10391.6872-0.1054-0.13631.0009-0.10030.810817.903334.8815228.1572
54.31570.18961.43031.34680.17272.20050.3750.39580.1554-0.2301-0.1996-0.2693-0.10340.099-0.17541.013-0.03310.20351.4035-0.02781.0703-59.6535-55.6887154.7705
63.9586-0.50091.56222.3697-0.53551.8524-0.21020.41350.2832-0.0961-0.0319-0.0753-0.2298-0.07030.24211.3747-0.15360.12161.131-0.16481.077-8.47071.2012155.0104
72.2968-1.03820.0243.5462-0.36532.8545-0.132-0.2069-0.21630.22040.41060.36090.5326-0.0694-0.27861.3914-0.2051-0.03751.2047-0.04911.1185-26.6019-32.3137184.2115
81.4101-0.9328-0.55065.174-1.76322.5836-0.0049-0.32620.17950.67920.1096-0.0545-0.11970.1797-0.10470.9922-0.1907-0.08611.1329-0.08720.993326.077118.9193185.0772
94.0079-0.2518-0.4581.8171-1.45731.3171-0.024-1.53182.2722-0.2793-0.5449-0.93430.0978-0.1940.56891.46440.24520.05911.7294-0.19272.288-40.0989-40.827772.7273
102.06520.7151-1.10231.46321.22172.70321.25371.58263.20010.23210.17890.12190.4365-0.8211-1.43261.3820.2353-0.08632.32190.32522.5065-12.5365-14.9783269.0892
111.2052-0.22640.34921.51560.47190.29731.03810.3792-0.3995-0.2295-0.60430.39360.70390.0829-0.43382.41260.1735-0.80671.5161-0.31952.226741.167739.5489266.9762
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 1:326
2X-RAY DIFFRACTION2chain B and resseq 1:326
3X-RAY DIFFRACTION3chain C and resseq 1:326
4X-RAY DIFFRACTION4chain D and resseq 1:326
5X-RAY DIFFRACTION5chain A and resseq 2012:2361
6X-RAY DIFFRACTION6chain B and resseq 2012:2361
7X-RAY DIFFRACTION7chain C and resseq 2012:2361
8X-RAY DIFFRACTION8chain D and resseq 2012:2361
9X-RAY DIFFRACTION9chain A and resseq 1002:1161
10X-RAY DIFFRACTION10chain C and resseq 1002:1161
11X-RAY DIFFRACTION11chain D and resseq 1002:1161

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