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- PDB-9c6e: High-resolution structure of bovine (3-367)Arrestin-1 in a pre-ac... -

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Basic information

Entry
Database: PDB / ID: 9c6e
TitleHigh-resolution structure of bovine (3-367)Arrestin-1 in a pre-activated conformation
ComponentsS-arrestin
KeywordsSIGNALING PROTEIN / GPCR / RHODOPSIN / PHOTOTRANSDUCTION / VISION
Function / homology
Function and homology information


opsin binding / Inactivation, recovery and regulation of the phototransduction cascade / G protein-coupled receptor internalization / response to light stimulus / photoreceptor outer segment / photoreceptor inner segment / phosphoprotein binding / G protein-coupled receptor binding / signal transduction / identical protein binding ...opsin binding / Inactivation, recovery and regulation of the phototransduction cascade / G protein-coupled receptor internalization / response to light stimulus / photoreceptor outer segment / photoreceptor inner segment / phosphoprotein binding / G protein-coupled receptor binding / signal transduction / identical protein binding / membrane / cytosol
Similarity search - Function
Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / 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 / Immunoglobulin E-set
Similarity search - Domain/homology
GLYCOLIC ACID / S-arrestin
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å
AuthorsSalom, D. / Palczewski, K. / Kiser, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)EY034519 United States
CitationJournal: Biochemistry / Year: 2025
Title: Insights into the Activation and Self-Association of Arrestin-1.
Authors: Salom, D. / Kiser, P.D. / Palczewski, K.
History
DepositionJun 7, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Jan 1, 2025Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 29, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S-arrestin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8614
Polymers40,6701
Non-polymers1913
Water9,782543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.560, 74.760, 79.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein S-arrestin / 48 kDa protein / Retinal S-antigen / S-AG / Rod photoreceptor arrestin


Mass: 40669.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Lys-C cleavage product of bovine arrestin-1 / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P08168
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-GOA / GLYCOLIC ACID / HYDROXYACETIC ACID / HYDROXYETHANOIC ACID


Mass: 76.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 543 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M imidazole, 0.1 M MES pH 6.5, 10% PEG 4000, 20% glycerol, 20 mM sodium formate; 20 mM ammonium acetate; 20 mM sodium citrate tribasic dihydrate; 20 mM potassium sodium tartrate ...Details: 0.1 M imidazole, 0.1 M MES pH 6.5, 10% PEG 4000, 20% glycerol, 20 mM sodium formate; 20 mM ammonium acetate; 20 mM sodium citrate tribasic dihydrate; 20 mM potassium sodium tartrate tetrahydrate; 20 mM sodium oxamate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 78726 / % possible obs: 99.7 % / Redundancy: 15.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Net I/σ(I): 13.2
Reflection shellResolution: 1.4→1.48 Å / Rmerge(I) obs: 2.874 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 11792 / CC1/2: 0.398

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.4→42.19 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.499 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.055
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1798 3937 5.001 %RANDOM
Rwork0.1406 74788 --
all0.143 ---
obs-78725 99.707 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.644 Å2
Baniso -1Baniso -2Baniso -3
1--1.48 Å2-0 Å20 Å2
2--1.975 Å2-0 Å2
3----0.495 Å2
Refinement stepCycle: LAST / Resolution: 1.4→42.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2729 0 12 543 3284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0123004
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162924
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.664108
X-RAY DIFFRACTIONr_angle_other_deg0.4171.5716788
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1025397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.403518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.98710529
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.21310114
X-RAY DIFFRACTIONr_chiral_restr0.060.2480
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023523
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02635
X-RAY DIFFRACTIONr_nbd_refined0.2440.2473
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.22596
X-RAY DIFFRACTIONr_nbtor_refined0.1670.21463
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21666
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2378
X-RAY DIFFRACTIONr_metal_ion_refined0.3120.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0910.211
X-RAY DIFFRACTIONr_nbd_other0.1710.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1590.227
X-RAY DIFFRACTIONr_mcbond_it1.442.5581518
X-RAY DIFFRACTIONr_mcbond_other1.442.5581518
X-RAY DIFFRACTIONr_mcangle_it2.0134.5961927
X-RAY DIFFRACTIONr_mcangle_other2.0134.5981928
X-RAY DIFFRACTIONr_scbond_it1.5032.9261486
X-RAY DIFFRACTIONr_scbond_other1.5032.9261487
X-RAY DIFFRACTIONr_scangle_it2.1075.2152175
X-RAY DIFFRACTIONr_scangle_other2.1075.2142176
X-RAY DIFFRACTIONr_lrange_it4.59433.263408
X-RAY DIFFRACTIONr_lrange_other4.36231.8693354
X-RAY DIFFRACTIONr_rigid_bond_restr2.64935928
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.4-1.4360.3412800.32453090.32557630.8940.90696.98070.324
1.436-1.4760.2872800.26653200.26756120.9260.93899.78620.253
1.476-1.5180.232730.22352040.22354780.9540.9699.98170.204
1.518-1.5650.2282670.18450470.18653150.9620.97599.98120.162
1.565-1.6160.1892570.15149060.15351640.9740.98399.98060.126
1.616-1.6730.1832500.13647290.13949810.9770.98799.95990.114
1.673-1.7360.1562420.11445950.11648370.9840.9921000.093
1.736-1.8070.1392290.10443930.10646370.9860.99399.67650.085
1.807-1.8870.152250.09842530.10144800.9870.99499.95540.084
1.887-1.9790.1632130.09440430.09742560.9840.9951000.083
1.979-2.0860.1442050.09438810.09640870.9860.99599.97550.087
2.086-2.2120.1491920.09336680.09538610.9860.99599.97410.088
2.212-2.3640.1561820.10734480.10936350.9820.99399.86240.105
2.364-2.5530.181690.12732200.1333960.9810.99199.79390.128
2.553-2.7950.1831570.1329840.13331410.9790.991000.138
2.795-3.1240.1781440.1327250.13228690.9790.9891000.144
3.124-3.6040.1571260.13923940.1425200.9860.9891000.159
3.604-4.4050.1891090.1520750.15221860.9790.98699.90850.182
4.405-6.1960.215850.16516220.16717090.9710.98299.8830.213
6.196-42.190.181520.2229720.2210260.9810.96699.80510.292

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