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- PDB-5w0p: Crystal structure of rhodopsin bound to visual arrestin determine... -

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Basic information

Entry
Database: PDB / ID: 5w0p
TitleCrystal structure of rhodopsin bound to visual arrestin determined by X-ray free electron laser
Components(Endolysin,Rhodopsin,S-arrestin) x 2
KeywordsSIGNALING PROTEIN / rhodopsin / GPCR / arrestin / GRK / phosphorylation codes / membrane proteins
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 / Endolysin / Rhodopsin / S-arrestin
Similarity search - Component
Biological speciesEnterobacteria phage RB55 (virus)
Homo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 3.013 Å
AuthorsZhou, X.E. / He, Y. / de Waal, P.W. / Gao, X. / Kang, Y. / Van Eps, N. / Yin, Y. / Pal, K. / Goswami, D. / White, T.A. ...Zhou, X.E. / He, Y. / de Waal, P.W. / Gao, X. / Kang, Y. / Van Eps, N. / Yin, Y. / Pal, K. / Goswami, D. / White, T.A. / Barty, A. / Latorraca, N.R. / Chapman, H.N. / Hubbell, W.L. / Dror, R.O. / Stevens, R.C. / Cherezov, V. / Gurevich, V.V. / Griffin, P.R. / Ernst, O.P. / Melcher, K. / Xu, H.E.
Funding support United States, China, Canada, 12items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK071662 United States
Ministry of Science and Technology (MoST, China)2012ZX09301001 China
Ministry of Science and Technology (MoST, China)2012CB910403 China
Ministry of Science and Technology (MoST, China)2013CB910600 China
Ministry of Science and Technology (MoST, China)XDB08020303 China
Ministry of Science and Technology (MoST, China)2013ZX09507001 China
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM108635 United States
National Institutes of Health/National Eye Institute (NIH/NEI)RO1 EY011500 United States
American Asthma Foundation United States
Jay and Betty Van Andel Foundation United States
Canada Excellence Research Chairs program Canada
Anne and Max Tanenbaum Chair in Neuroscience Canada
CitationJournal: Cell / Year: 2017
Title: Identification of Phosphorylation Codes for Arrestin Recruitment by G Protein-Coupled Receptors.
Authors: Zhou, X.E. / He, Y. / de Waal, P.W. / Gao, X. / Kang, Y. / Van Eps, N. / Yin, Y. / Pal, K. / Goswami, D. / White, T.A. / Barty, A. / Latorraca, N.R. / Chapman, H.N. / Hubbell, W.L. / Dror, R. ...Authors: Zhou, X.E. / He, Y. / de Waal, P.W. / Gao, X. / Kang, Y. / Van Eps, N. / Yin, Y. / Pal, K. / Goswami, D. / White, T.A. / Barty, A. / Latorraca, N.R. / Chapman, H.N. / Hubbell, W.L. / Dror, R.O. / Stevens, R.C. / Cherezov, V. / Gurevich, V.V. / Griffin, P.R. / Ernst, O.P. / Melcher, K. / Xu, H.E.
History
DepositionMay 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.2Nov 21, 2018Group: Data collection
Category: pdbx_serial_crystallography_data_reduction / pdbx_serial_crystallography_measurement ...pdbx_serial_crystallography_data_reduction / pdbx_serial_crystallography_measurement / pdbx_serial_crystallography_sample_delivery / pdbx_serial_crystallography_sample_delivery_injection
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)405,6308
Polymers403,9324
Non-polymers1,6984
Water0
1
A: Endolysin,Rhodopsin,S-arrestin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,4472
Polymers101,0231
Non-polymers4241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endolysin,Rhodopsin,S-arrestin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,4472
Polymers101,0231
Non-polymers4241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Endolysin,Rhodopsin,S-arrestin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,3672
Polymers100,9431
Non-polymers4241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Endolysin,Rhodopsin,S-arrestin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,3672
Polymers100,9431
Non-polymers4241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 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: 101023.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage RB55 (virus), (gene. exp.) Homo sapiens (human), (gene. exp.) Mus musculus (house mouse)
Gene: e, RB55_p125, RHO, OPN2, Sag / Production host: Homo sapiens (human)
References: UniProt: A0A097J792, UniProt: P08100, UniProt: P20443, UniProt: P00720*PLUS, lysozyme
#2: 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: 100943.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage RB55 (virus), (gene. exp.) Homo sapiens (human), (gene. exp.) Mus musculus (house mouse)
Gene: e, RB55_p125, RHO, OPN2, Sag / Production host: Homo sapiens (human)
References: UniProt: A0A097J792, UniProt: P08100, UniProt: P20443, UniProt: P00720*PLUS, lysozyme
#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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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: 3.33 Å3/Da / Density % sol: 63.06 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5 / Details: PEG 400, magnesium acetate, sodium acetate.

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.33 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: 1.33 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 76360 / % possible obs: 72.4 % / Redundancy: 287 % / CC1/2: 0.988 / Net I/σ(I): 4.5
Reflection shellResolution: 3→3.1 Å / CC1/2: 0.233
Serial crystallography measurementFocal spot size: 1 µm2 / Photons per pulse: 1.0E+20 Tphotons/pulse / Pulse duration: 48 fsec. / Pulse photon energy: 1.78 keV / XFEL pulse repetition rate: 120 Hz
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionCarrier solvent: LCP / Flow rate: 0.2 µL/min / Injector diameter: 50 µm / Injector nozzle: 50
Serial crystallography data reductionCrystal hits: 22462 / Frames failed index: 17730 / Frames total: 5000000

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZWJ

4zwj


Resolution: 3.013→30.03 Å / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.17 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2722 3761 4.93 %
Rwork0.2343 --
obs0.2369 76360 70.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.013→30.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25864 0 112 0 25976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00526612
X-RAY DIFFRACTIONf_angle_d0.84536174
X-RAY DIFFRACTIONf_dihedral_angle_d10.8269700
X-RAY DIFFRACTIONf_chiral_restr0.0394154
X-RAY DIFFRACTIONf_plane_restr0.0074544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0256-3.07770.296890.3534213X-RAY DIFFRACTION4
3.0777-3.13360.3521210.3376459X-RAY DIFFRACTION9
3.1336-3.19380.2956290.3492715X-RAY DIFFRACTION14
3.1938-3.25890.4258650.354992X-RAY DIFFRACTION19
3.2589-3.32970.4023660.37861369X-RAY DIFFRACTION26
3.3297-3.4070.3888950.36741828X-RAY DIFFRACTION35
3.407-3.49210.36331290.37942435X-RAY DIFFRACTION46
3.4921-3.58640.39281720.36793368X-RAY DIFFRACTION64
3.5864-3.69170.4182540.37044917X-RAY DIFFRACTION93
3.6917-3.81070.3712330.33425041X-RAY DIFFRACTION95
3.8107-3.94660.32862740.30945054X-RAY DIFFRACTION95
3.9466-4.10420.32972480.29345029X-RAY DIFFRACTION95
4.1042-4.29050.2782710.26345079X-RAY DIFFRACTION95
4.2905-4.5160.27662860.25415046X-RAY DIFFRACTION95
4.516-4.79790.26092840.22425069X-RAY DIFFRACTION95
4.7979-5.16660.24072550.21535087X-RAY DIFFRACTION95
5.1666-5.68340.30892560.23725129X-RAY DIFFRACTION95
5.6834-6.49850.29242530.23985156X-RAY DIFFRACTION95
6.4985-8.16020.22143020.19885169X-RAY DIFFRACTION94
8.1602-30.03130.22742590.17665431X-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)
10.06910.20040.08070.0121-0.00920.06820.0297-0.2864-0.13180.2406-0.3905-0.01340.113-0.50202.7681-0.6950.08081.7211-0.14951.7467-18.089414.6447187.6674
20.07130.09840.04580.0923-0.0429-0.01210.0039-0.5672-0.076-0.1465-0.0133-0.015-0.169-0.122701.51090.42630.00071.1283-0.06651.1107-36.141121.8835227.1311
3-0.56040.21660.1279-0.17590.00680.1678-0.35190.19190.134-0.33790.20720.0699-0.1565-0.1549-01.33580.1916-0.06881.2894-0.09421.301-30.077232.5115262.3119
40.0787-0.088-0.0006-0.16140.01480.0318-0.0540.03670.38110.5292-0.3426-0.36670.1952-0.169100.91420.67120.02951.5771-0.30441.7484-14.5649-14.5801267.3997
50.1203-0.12320.22990.25750.02970.10120.1220.3664-0.00610.22710.205-0.1667-0.5291-0.3364-01.8388-0.14570.06170.78590.09031.0011-33.7386-18.017226.8803
6-0.1899-0.3694-0.04170.0324-0.04530.0416-0.63710.1113-0.01510.30260.5137-0.01280.3079-0.0721-01.3510.07070.03631.317-0.06781.0989-32.0302-14.4524189.3309
70.06310.312-0.06570.1097-0.06680.0962-0.4993-0.17180.0940.19870.27570.56640.53040.126601.7433-0.39150.2711.4834-0.09121.1811-22.6341-50.3089189.2298
80.0196-0.2740.08120.11370.07660.1022-0.3164-0.29030.74030.2159-0.16-0.06340.8073-0.241602.03840.6571-0.48052.116-0.1821.5306-38.8704-45.110574.5022
90.1362-0.02490.12310.063-0.01960.0956-0.13710.21190.48220.35530.32500.1184-0.0449-01.01220.07880.19341.41340.14471.1819-45.7698-63.2714114.226
10-0.1497-0.3184-0.0758-0.25330.3211-0.06020.2310.01090.1010.2154-0.0311-0.0337-0.31140.047100.8930.05070.04991.36380.02081.1961-56.346-57.2722149.5034
11-0.1819-0.00890.00990.03050.00040.0150.1741-0.0610.5274-0.14450.1073-0.04120.0647-0.129701.8855-0.1190.98752.669-0.6191.7897-7.7618-43.5689157.8005
120.1406-0.077-0.06960.14180.13210.0110.9074-1.0534-0.1418-0.0682-0.3112-0.12330.2566-0.96670-2.05722.32210.3663-0.3641-0.48360.884-5.8363-60.7774113.9737
13-0.01430.1186-0.0405-0.1322-0.32840.4029-0.0748-0.20670.167-0.1738-0.10880.03410.12130.6587-01.3440.26740.07890.95730.02350.83225.3696-55.170576.5168
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resseq -159:33 )
2X-RAY DIFFRACTION2chain A and (resseq 34:277 )
3X-RAY DIFFRACTION3chain A and (resseq 278:2362 )
4X-RAY DIFFRACTION4chain B and (resseq -159:14 )
5X-RAY DIFFRACTION5chain B and resseq 15:277
6X-RAY DIFFRACTION6chain B and resseq 278:2189
7X-RAY DIFFRACTION7chain B and resseq 2190:2361
8X-RAY DIFFRACTION8chain C and resseq -159:33
9X-RAY DIFFRACTION9chain C and resseq 34:277
10X-RAY DIFFRACTION10chain C and resseq 278:2361
11X-RAY DIFFRACTION11chain D and resseq -85:14
12X-RAY DIFFRACTION12chain D and resseq 15:277
13X-RAY DIFFRACTION13chain D and resseq 278:2361

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