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- PDB-7jsm: CRYSTAL STRUCTURE OF NATIVE BOVINE ARRESTIN 1 -

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Basic information

Entry
Database: PDB / ID: 7jsm
TitleCRYSTAL STRUCTURE OF NATIVE BOVINE ARRESTIN 1
ComponentsS-arrestin
KeywordsPROTEIN BINDING / GPCR / rhodopsin / phototransduction / basal state
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
Immunoglobulin-like - #840 / Immunoglobulin-like - #640 / 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 ...Immunoglobulin-like - #840 / Immunoglobulin-like - #640 / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsSander, C.L. / Palczewski, K. / Kiser, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)EY009339 United States
CitationJournal: Structure / Year: 2022
Title: Structural evidence for visual arrestin priming via complexation of phosphoinositols.
Authors: Sander, C.L. / Luu, J. / Kim, K. / Furkert, D. / Jang, K. / Reichenwallner, J. / Kang, M. / Lee, H.J. / Eger, B.T. / Choe, H.W. / Fiedler, D. / Ernst, O.P. / Kim, Y.J. / Palczewski, K. / Kiser, P.D.
History
DepositionAug 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 3, 2021Group: Database references / Category: citation / citation_author
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.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 16, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-arrestin
B: S-arrestin
C: S-arrestin
D: S-arrestin


Theoretical massNumber of molelcules
Total (without water)181,3394
Polymers181,3394
Non-polymers00
Water2,882160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.175, 186.967, 90.322
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA9 - 3859 - 385
21LEULEUBB9 - 3859 - 385
12LEULEUAA9 - 3859 - 385
22LEULEUCC9 - 3859 - 385
13LEULEUAA9 - 3859 - 385
23LEULEUDD9 - 3859 - 385
14ASNASNBB9 - 3849 - 384
24ASNASNCC9 - 3849 - 384
15METMETBB9 - 4029 - 402
25METMETDD9 - 4029 - 402
16ASNASNCC9 - 3849 - 384
26ASNASNDD9 - 3849 - 384

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 45334.781 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P08168
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O

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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: 3.89 Å3/Da / Density % sol: 68.4 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Bis-Tris propane, 35% 2-Ethoxyethanol, 0.001 M Magnesium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 98577 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 72.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.93
Reflection shellResolution: 2.5→2.65 Å / Rmerge(I) obs: 1.721 / Num. unique obs: 15684 / CC1/2: 0.52 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3UGX

3ugx


Resolution: 2.5→49.04 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / SU B: 22.876 / SU ML: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.269 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2328 4928 5 %RANDOM
Rwork0.2076 ---
obs0.2088 93643 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 157.51 Å2 / Biso mean: 72.077 Å2 / Biso min: 37.98 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å2-0 Å2-0 Å2
2--1.65 Å2-0 Å2
3----2.85 Å2
Refinement stepCycle: final / Resolution: 2.5→49.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11748 0 0 160 11908
Biso mean---61.48 -
Num. residues----1497
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01311988
X-RAY DIFFRACTIONr_bond_other_d0.0030.01711436
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.64916257
X-RAY DIFFRACTIONr_angle_other_deg1.1921.57526590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2451488
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.62522.73575
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.044152134
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3131568
X-RAY DIFFRACTIONr_chiral_restr0.0610.21600
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213144
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022336
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A101940.14
12B101940.14
21A108980.08
22C108980.08
31A103150.13
32D103150.13
41B100270.12
42C100270.12
51B112840.09
52D112840.09
61C101540.12
62D101540.12
LS refinement shellResolution: 2.5→2.564 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.391 356 -
Rwork0.414 6819 -
obs--99.49 %
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)
14.6214-0.80480.62960.1432-0.11950.17280.01630.24080.1028-0.005-0.046-0.0379-0.00530.01220.02960.00690.00070.03210.10120.02230.196291.07136.183-3.196
22.24930.7597-0.97731.9706-1.23783.4733-0.0078-0.0835-0.3336-0.03980.06020.16580.4756-0.3207-0.05250.101-0.0163-0.05260.1233-0.04340.169930.65721.635-0.121
30.248-0.9855-0.25324.68740.94170.4432-0.0724-0.0482-0.06990.4320.0290.1415-0.00280.00330.04340.1017-0.0139-0.01630.1643-0.00150.124447.156-10.25325.352
41.76111.0621-1.33572.7611-1.6533.44340.0723-0.09220.15780.145-0.0572-0.3241-0.23080.3546-0.01510.0499-0.006-0.04980.1125-0.04830.150157.48150.1122.528
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 386
2X-RAY DIFFRACTION1A501 - 549
3X-RAY DIFFRACTION1D526
4X-RAY DIFFRACTION2B8 - 402
5X-RAY DIFFRACTION2B501 - 525
6X-RAY DIFFRACTION3C9 - 385
7X-RAY DIFFRACTION3C508 - 528
8X-RAY DIFFRACTION4D9 - 403

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