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- PDB-7f1w: X-ray crystal structure of visual arrestin complexed with inosito... -

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Basic information

Entry
Database: PDB / ID: 7f1w
TitleX-ray crystal structure of visual arrestin complexed with inositol hexaphosphate
ComponentsS-arrestin
KeywordsSIGNALING PROTEIN
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 / G protein-coupled receptor binding / phosphoprotein binding / signal transduction / membrane ...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 / G protein-coupled receptor binding / phosphoprotein binding / signal transduction / membrane / identical protein binding / 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
INOSITOL HEXAKISPHOSPHATE / S-arrestin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.097 Å
AuthorsKang, M. / Jang, K. / Eger, B.T. / Ernst, O.P. / Choe, H.W. / Kim, Y.J.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2017M3A9F6029733 Korea, Republic Of
National Research Foundation (NRF, Korea)2017R1B5A2086096 Korea, Republic Of
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
DepositionJun 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
D: S-arrestin
C: S-arrestin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,3197
Polymers181,3394
Non-polymers1,9803
Water0
1
A: S-arrestin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9952
Polymers45,3351
Non-polymers6601
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-4 kcal/mol
Surface area18090 Å2
MethodPISA
2
B: S-arrestin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9952
Polymers45,3351
Non-polymers6601
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-4 kcal/mol
Surface area19040 Å2
MethodPISA
3
D: S-arrestin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9952
Polymers45,3351
Non-polymers6601
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint-5 kcal/mol
Surface area18850 Å2
MethodPISA
4
C: S-arrestin


Theoretical massNumber of molelcules
Total (without water)45,3351
Polymers45,3351
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.849, 190.465, 190.473
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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 (cattle) / References: UniProt: P08168
#2: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H18O24P6 / Feature type: SUBJECT OF INVESTIGATION
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: 4.2 Å3/Da / Density % sol: 73.7 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 7
Details: 40 mM PIPES pH 7.2/0.6 M KCl/22% ethylene glycol/5.7% polyethylene glycol 6000/13% polyethylene glycol 200/4% polyethylene glycol 1000
PH range: 6.8-7.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.097→46.195 Å / Num. obs: 55228 / % possible obs: 99 % / Redundancy: 4.6 % / CC1/2: 0.993 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.04 / Net I/σ(I): 11.6
Reflection shellResolution: 3.097→3.208 Å / Rmerge(I) obs: 0.417 / Num. unique obs: 5331 / CC1/2: 0.775 / Rpim(I) all: 0.219 / Rrim(I) all: 0.475

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CF1

1cf1


Resolution: 3.097→46.195 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2406 2757 4.99 %RANDON
Rwork0.2153 ---
obs0.2165 55209 99.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.097→46.195 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11360 0 108 0 11468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211692
X-RAY DIFFRACTIONf_angle_d0.55515874
X-RAY DIFFRACTIONf_dihedral_angle_d9.4557174
X-RAY DIFFRACTIONf_chiral_restr0.0461850
X-RAY DIFFRACTIONf_plane_restr0.0051994
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0972-3.15060.36461320.36122409X-RAY DIFFRACTION94
3.1506-3.20790.33141530.312636X-RAY DIFFRACTION100
3.2079-3.26960.33031430.29182624X-RAY DIFFRACTION100
3.2696-3.33630.28461340.28772599X-RAY DIFFRACTION100
3.3363-3.40880.3371220.28882644X-RAY DIFFRACTION100
3.4088-3.48810.30631410.27332591X-RAY DIFFRACTION100
3.4881-3.57530.27561350.2492633X-RAY DIFFRACTION100
3.5753-3.67190.27381380.25782616X-RAY DIFFRACTION100
3.6719-3.77990.26121470.24092602X-RAY DIFFRACTION100
3.7799-3.90180.26771480.23082649X-RAY DIFFRACTION100
3.9018-4.04120.25661330.22782611X-RAY DIFFRACTION100
4.0412-4.20290.25341240.21672656X-RAY DIFFRACTION100
4.2029-4.39410.19891420.18662638X-RAY DIFFRACTION100
4.3941-4.62550.21181430.16962609X-RAY DIFFRACTION100
4.6255-4.9150.17781440.15272641X-RAY DIFFRACTION100
4.915-5.2940.19351400.16042676X-RAY DIFFRACTION100
5.294-5.82580.20891280.18532658X-RAY DIFFRACTION100
5.8258-6.66670.21261370.20072679X-RAY DIFFRACTION100
6.6667-8.39110.21471490.19112675X-RAY DIFFRACTION99
8.3911-46.1950.22131240.20682606X-RAY DIFFRACTION93
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)
11.46471.38661.62362.26111.21111.7281-0.1711-0.05990.1162-0.2715-0.02710.2262-1.11550.73390.05820.5811-0.0532-0.06160.54340.15070.4372-26.5417-19.328872.9411
22.67261.6930.07090.9289-0.31352.65080.049-0.1240.05030.2794-0.09130.1306-0.4860.23150.03220.4081-0.0159-0.00540.33710.02990.2919-29.0917-27.581381.5414
30.4651-0.94520.70512.8339-1.30511.2345-0.0221-0.45860.00050.35630.2417-0.3315-0.41960.0266-0.27810.2979-0.03930.04310.65280.08570.4412-27.0301-32.644975.941
41.6890.42551.14552.7784-0.43153.9134-0.04360.10390.4552-0.0927-0.0633-0.0425-0.3050.06720.0470.4416-0.0562-0.01880.57510.08070.4429-30.7188-24.998570.9308
50.8849-0.1510.03241.62010.29952.6643-0.1004-0.17210.03810.3192-0.09890.0267-0.78550.56120.31680.38650.0118-0.0380.54350.10430.4373-31.2919-28.140272.2802
63.0870.72820.57873.7312-0.22021.6036-0.13470.53650.1662-0.451-0.04750.0451-0.4220.71380.13920.5312-0.05290.05330.36410.08550.2484-39.9185-21.203630.6569
72.944-0.68760.92350.5163-1.2893.2464-0.1010.19380.2491-0.10890.11130.026-0.3506-0.44890.04790.5819-0.07630.05070.4972-0.00290.4507-45.0385-17.681133.3983
80.6621-0.06280.64020.589-0.44332.3690.0886-0.0739-0.22490.22710.25090.2163-0.7136-0.3791-0.27210.7993-0.0197-0.00520.51880.08950.416-44.5554-16.759940.6544
92.2329-1.42150.35673.10631.33714.1675-0.38170.0850.25610.52080.421-0.08460.0873-0.2766-0.01910.5991-0.01110.0950.53080.10130.5349-39.3854-23.328557.4882
100.0719-0.24380.05751.4072-1.33721.9696-0.1568-0.3478-0.08560.22810.04360.0666-0.5443-0.2456-0.27010.42360.05260.05830.44730.03010.3456-50.117-21.841534.7263
112.16591.6193.02981.05251.26635.6589-0.1754-0.24190.3362-0.0623-0.1459-0.0689-0.8467-0.25340.17920.6979-0.0419-0.06650.53590.06990.4883-29.8733-15.842259.5252
121.724-0.5066-0.17763.1642-0.02142.83190.15650.4336-0.2095-0.6003-0.309-0.57510.24510.68640.01920.52440.1030.10210.72080.01360.5368-21.7794-39.231-12.7386
130.65-0.4157-0.4982.05970.46871.53060.09030.0210.06450.2409-0.1057-0.0894-0.53180.0028-0.00210.585-0.089-0.05610.44720.0610.3619-34.1275-12.71247.2145
141.1073-1.6515-1.93583.1552.09523.41820.1164-0.17370.3095-0.08760.3974-0.7841-0.42331.0002-0.27770.623-0.1728-0.02210.67450.03870.5459-26.8031-16.16871.4884
154.3592-0.55721.32791.4910.54940.92170.13110.0667-0.3626-0.0531-0.1163-0.03860.00960.1407-0.020.3620.10880.0120.5102-0.02060.275625.3324-50.990516.2013
164.3055-0.04842.31382.6768-0.81111.3717-0.5701-0.72750.23750.41630.4685-0.0029-0.4085-0.4409-0.15680.39680.2070.00360.59-0.04760.444124.2802-41.718115.9754
172.19650.4943-0.52821.67090.1170.8807-0.0322-0.04610.19-0.1505-0.01230.09770.0308-0.01340.00710.34830.0891-0.02490.4713-0.00160.359623.1553-46.746212.7645
187.91540.4839-1.02520.62970.68091.04260.07390.1490.85460.03860.1735-0.02440.1836-0.2309-0.28010.41670.0369-0.07520.50440.03750.441110.1692-50.576715.9109
192.53990.33861.18980.3723-0.39031.1787-0.0168-0.1949-0.391-0.22780.15770.18830.1884-0.1784-0.09890.3610.0197-0.08190.3694-0.03940.4776-20.7691-54.33327.0957
204.93040.7496-0.08991.10660.39740.1396-0.31670.7484-0.7998-0.26980.1986-0.04140.25550.13970.15190.55540.021-0.10770.5946-0.05060.5177-14.3863-56.36123.3792
214.039-0.31171.98670.0557-0.8230.380.22260.3816-0.5286-0.0467-0.07050.2920.0770.1173-0.16810.47490.0869-0.0390.5264-0.10070.48390.1997-54.38087.7693
222.0323-1.4411-1.54512.00810.53781.7095-0.2931-0.2990.34760.8325-0.16561.09120.3316-0.46720.27550.711-0.13950.28890.9016-0.25221.085-62.3829-34.695734.0474
232.68350.412-0.49260.1856-0.46930.9142-0.0515-0.36990.51570.225-0.30531.3533-0.1759-0.6522-0.20720.5402-0.05450.18070.9058-0.2561.433-69.489-34.195328.5225
241.29270.3667-0.40321.67960.50312.5135-0.02620.0268-0.2690.2721-0.3480.5720.0754-0.27620.17120.4016-0.1769-0.00210.5709-0.00820.7743-52.1182-50.112520.9974
251.795-0.9339-0.48863.1771.89722.5934-0.1463-0.0807-0.48990.65840.0314-0.07240.4465-0.01840.12010.5216-0.1525-0.00860.49040.12070.6393-42.2176-60.189819.0147
261.09-0.5956-0.91881.9808-0.03680.8535-0.5313-0.5574-0.7640.18810.19470.8985-0.1205-0.21860.39890.918-0.09020.44381.04640.00191.1022-66.238-49.648134.2154
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 40 )
2X-RAY DIFFRACTION2chain 'A' and (resid 41 through 67 )
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 101 )
4X-RAY DIFFRACTION4chain 'A' and (resid 102 through 154 )
5X-RAY DIFFRACTION5chain 'A' and (resid 155 through 188 )
6X-RAY DIFFRACTION6chain 'A' and (resid 189 through 219 )
7X-RAY DIFFRACTION7chain 'A' and (resid 220 through 247 )
8X-RAY DIFFRACTION8chain 'A' and (resid 248 through 286 )
9X-RAY DIFFRACTION9chain 'A' and (resid 287 through 322 )
10X-RAY DIFFRACTION10chain 'A' and (resid 323 through 346 )
11X-RAY DIFFRACTION11chain 'A' and (resid 347 through 385 )
12X-RAY DIFFRACTION12chain 'B' and (resid 10 through 178 )
13X-RAY DIFFRACTION13chain 'B' and (resid 179 through 336 )
14X-RAY DIFFRACTION14chain 'B' and (resid 337 through 385 )
15X-RAY DIFFRACTION15chain 'C' and (resid 9 through 67 )
16X-RAY DIFFRACTION16chain 'C' and (resid 68 through 101 )
17X-RAY DIFFRACTION17chain 'C' and (resid 102 through 165 )
18X-RAY DIFFRACTION18chain 'C' and (resid 166 through 188 )
19X-RAY DIFFRACTION19chain 'C' and (resid 189 through 247 )
20X-RAY DIFFRACTION20chain 'C' and (resid 248 through 280 )
21X-RAY DIFFRACTION21chain 'C' and (resid 281 through 386 )
22X-RAY DIFFRACTION22chain 'D' and (resid 11 through 77 )
23X-RAY DIFFRACTION23chain 'D' and (resid 78 through 130 )
24X-RAY DIFFRACTION24chain 'D' and (resid 131 through 219 )
25X-RAY DIFFRACTION25chain 'D' and (resid 220 through 356 )
26X-RAY DIFFRACTION26chain 'D' and (resid 357 through 384 )

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