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- PDB-5dgy: Crystal structure of rhodopsin bound to visual arrestin -

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Basic information

Entry
Database: PDB / ID: 5dgy
TitleCrystal structure of rhodopsin bound to visual arrestin
ComponentsEndolysin,Rhodopsin,S-arrestin
KeywordsSIGNALING PROTEIN / GPCR / rhodopsin / arrestin
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7.7 Å
AuthorsZhou, X.E. / Gao, X. / Kang, Y. / He, Y. / de Waal, P.W. / Suino-Powell, K.M. / Wang, M. / Melcher, K. / Xu, H.E.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK071662 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)ACB-12002 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)AGM-12006 United States
Michigan Economic Development Corporation and the Michigan Technology Tri-Corridor085P1000817 United States
CitationJournal: Sci Data / Year: 2016
Title: X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex.
Authors: 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, ...Authors: 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.
History
DepositionAug 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2Aug 9, 2017Group: Database references / Derived calculations / Category: pdbx_related_exp_data_set / pdbx_struct_oper_list / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Aug 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 1.6Sep 27, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endolysin,Rhodopsin,S-arrestin
B: Endolysin,Rhodopsin,S-arrestin
C: Endolysin,Rhodopsin,S-arrestin
D: Endolysin,Rhodopsin,S-arrestin


Theoretical massNumber of molelcules
Total (without water)403,4444
Polymers403,4444
Non-polymers00
Water0
1
A: Endolysin,Rhodopsin,S-arrestin
C: Endolysin,Rhodopsin,S-arrestin


Theoretical massNumber of molelcules
Total (without water)201,7222
Polymers201,7222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endolysin,Rhodopsin,S-arrestin
D: Endolysin,Rhodopsin,S-arrestin


Theoretical massNumber of molelcules
Total (without water)201,7222
Polymers201,7222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.484, 107.258, 460.314
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain a
21chain b
31chain c
41chain d

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain aa0
211chain bb0
311chain cc0
411chain dd0

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Components

#1: Protein
Endolysin,Rhodopsin,S-arrestin / 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)
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: 3.32 Å3/Da / Density % sol: 62.99 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5 / Details: PEG400 / PH range: 5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.03317 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
Reflection twinOperator: k,h,-l / Fraction: 0.39
ReflectionResolution: 7.7→30 Å / Num. all: 6795 / Num. obs: 6795 / % possible obs: 97.5 % / Redundancy: 4.68 % / CC1/2: 1 / Rmerge(I) obs: 0.314 / Net I/σ(I): 3.79
Reflection shellResolution: 7.7→8.1 Å / Redundancy: 4.12 % / Rmerge(I) obs: 1.188 / Mean I/σ(I) obs: 1.08 / CC1/2: 0.81 / % possible all: 0.908

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZWJ

4zwj


Resolution: 7.7→29.978 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 51.16 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.3351 845 7.08 %Random selection
Rwork0.2853 11085 --
obs0.2877 6630 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 990.94 Å2 / Biso mean: 420.2679 Å2 / Biso min: 189.39 Å2
Refinement stepCycle: final / Resolution: 7.7→29.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24665 0 0 0 24665
Num. residues----3128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00825278
X-RAY DIFFRACTIONf_angle_d1.02134355
X-RAY DIFFRACTIONf_chiral_restr0.0453942
X-RAY DIFFRACTIONf_plane_restr0.0094325
X-RAY DIFFRACTIONf_dihedral_angle_d11.1539188
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A14919X-RAY DIFFRACTION5.663TORSIONAL
12B14919X-RAY DIFFRACTION5.663TORSIONAL
13C14919X-RAY DIFFRACTION5.663TORSIONAL
14D14919X-RAY DIFFRACTION5.663TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
7.7005-8.17380.33731420.3021826196893
8.1738-8.79010.33491340.28811847198193
8.7901-9.64780.34721370.28281870200793
9.6478-10.98320.33381370.26121863200093
10.9832-13.61790.27011400.25171848198893
13.6179-29.96320.38671510.32481831198292
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)
10.3759-0.91310.09820.8584-0.59850.2783-1.85251.37950.6552-0.02310.1861-1.04530.6458-0.0259-0.02093.15440.6416-0.14574.16320.64121.8598-43.4943-62.5898113.8718
21.2631-1.0869-0.13951.85370.33660.1448-1.4526-1.69111.65090.75161.216-0.2830.50340.29110.07762.6481-0.56320.82445.4050.27890.04917.1517-6.6536114.4764
30.53280.12930.31760.4817-0.10460.1233-0.8311-0.53551.05070.71950.044-0.9356-0.2395-0.471904.06380.1477-0.31783.6662-0.31412.3966-33.6466-16.8494230.9646
40.18750.17740.2077-0.02020.16150.2865-0.31570.0181.2152.0932-1.1591-1.023-0.91310.2683-0.01935.5829-1.2242-0.72314.58660.88131.746917.53434.2783231.615
5-0.12810.12810.12841.6927-1.5961.461-0.23740.6628-0.31680.47952.0868-1.07190.6987-2.09251.82112.50040.4032-0.16484.1826-0.81562.6149-58.3285-52.8481157.1819
6-0.05630.530.02310.50640.66320.2677-1.3190.92750.0564-0.2711.07990.71330.9128-1.0829-0.01473.1943-0.8389-0.41174.59730.62653.2676-7.85642.2452157.709
71.21981.2706-0.35230.56120.26150.34160.32760.34410.4277-1.3041-0.32630.6741-0.5121-0.1066-0.00964.1284-0.33380.38656.1897-0.73153.991-25.5182-31.3624187.3382
81.15550.64510.23020.16590.47390.82220.8299-0.1939-0.240.6463-0.4176-0.5379-1.5212-1.62010.4524.169-0.2620.15675.8659-0.74765.467526.759919.4474188.3436
90.0168-0.2744-0.0213-0.0180.0795-0.0037-0.4239-0.0971.2753-0.2302-0.0997-1.21410.0242-0.094-0.34356.38080.4441-0.15366.4766-0.17417.0563-38.6708-40.306174.7769
100.0597-0.16110.1068-0.1129-0.07720.0508-0.61160.73560.1346-0.49730.1734-1.7680.34250.7785-05.0545-0.1836-0.61725.30090.49833.3311-12.7982-15.9794272.8025
110.0702-0.1794-0.1708-0.06830.0940.4534-0.26330.30711.139-1.4429-0.6345-2.1002-0.47040.7277-1.02495.93090.6751-0.84165.90650.36536.191340.029538.5156270.9333
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resseq 1:326A1 - 326
2X-RAY DIFFRACTION2chain b and resseq 1:326b1 - 326
3X-RAY DIFFRACTION3chain c and resseq 1:326c1 - 326
4X-RAY DIFFRACTION4chain d and resseq 1:326d1 - 326
5X-RAY DIFFRACTION5chain a and resseq 1012:1361a1012 - 1361
6X-RAY DIFFRACTION6chain b and resseq 1012:1361b1012 - 1361
7X-RAY DIFFRACTION7chain c and resseq 1012:1361c1012 - 1361
8X-RAY DIFFRACTION8chain d and resseq 1012:1361d1012 - 1361
9X-RAY DIFFRACTION9chain a and resseq -159:0a-159 - 0
10X-RAY DIFFRACTION10chain c and resseq -159:0c-159 - 0
11X-RAY DIFFRACTION11chain d and resseq -159:0d-159 - 0

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