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- PDB-7mp0: CRYSTAL STRUCTURE OF NATIVE BOVINE ARRESTIN 1 IN COMPLEX WITH 1D-... -

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Basic information

Entry
Database: PDB / ID: 7mp0
TitleCRYSTAL STRUCTURE OF NATIVE BOVINE ARRESTIN 1 IN COMPLEX WITH 1D-MYO-INOSITOL 5-DIPHOSPHATE PENTAKISPHOSPHATE (5-PP IP5)
ComponentsS-arrestin
KeywordsPROTEIN BINDING / GPCR / rhodopsin / phototransduction / inositol / 5PP-IP5 / IP7
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
2-ETHOXYETHANOL / Chem-I7P / S-arrestin
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 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
DepositionMay 4, 2021Deposition 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,12910
Polymers181,3394
Non-polymers3,7906
Water95553
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)168.995, 186.822, 90.539
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
11LYSLYSAA9 - 3869 - 386
21LYSLYSBB9 - 3869 - 386
12LEULEUAA9 - 3859 - 385
22LEULEUCC9 - 3859 - 385
13ASNASNAA9 - 3849 - 384
23ASNASNDD9 - 3849 - 384
14LEULEUBB9 - 3859 - 385
24LEULEUCC9 - 3859 - 385
15LEULEUBB9 - 3859 - 385
25LEULEUDD9 - 3859 - 385
16LEULEUCC9 - 3859 - 385
26LEULEUDD9 - 3859 - 385

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: Chemical ChemComp-ETX / 2-ETHOXYETHANOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#3: Chemical
ChemComp-I7P / (1r,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl trihydrogen diphosphate / 1D-myo-inositol 5-diphosphate 1,2,3,4,6-pentakisphosphate


Mass: 740.015 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H19O27P7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.94 Å3/Da / Density % sol: 68.79 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Bis-tris propane pH 7, 35% 2-Ethoxyethanol, 0.001 M Magnesium acetate, 5 mM 1D-myo-inositol 5-diphosphate pentakisphosphate

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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 PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 88724 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Net I/σ(I): 18.16
Reflection shellResolution: 2.6→2.76 Å / Rmerge(I) obs: 1.772 / Mean I/σ(I) obs: 0.98 / Num. unique obs: 14073 / CC1/2: 0.611

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7JTB

7jtb


Resolution: 2.6→49.14 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU B: 12.171 / SU ML: 0.228 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.33 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2476 4431 5 %RANDOM
Rwork0.2215 ---
obs0.2227 84114 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 238.04 Å2 / Biso mean: 86.191 Å2 / Biso min: 39.39 Å2
Baniso -1Baniso -2Baniso -3
1-2.71 Å2-0 Å2-0 Å2
2--2.65 Å2-0 Å2
3----5.36 Å2
Refinement stepCycle: final / Resolution: 2.6→49.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11500 0 206 53 11759
Biso mean--198.09 64.19 -
Num. residues----1461
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01311930
X-RAY DIFFRACTIONr_bond_other_d0.0020.01711479
X-RAY DIFFRACTIONr_angle_refined_deg1.2271.66216239
X-RAY DIFFRACTIONr_angle_other_deg1.0421.57726543
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.41951450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.7222.585561
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.804152099
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2161568
X-RAY DIFFRACTIONr_chiral_restr0.0410.21588
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212944
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022488
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A101730.12
12B101730.12
21A108290.08
22C108290.08
31A103430.12
32D103430.12
41B100850.11
42C100850.11
51B107160.09
52D107160.09
61C103010.11
62D103010.11
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.427 320 -
Rwork0.412 5970 -
all-6290 -
obs--96.75 %

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