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

ID or keywords:

Entry

Database: PDB / ID: 7f1w

Title

X-ray crystal structure of visual arrestin complexed with inositol hexaphosphate

Components

S-arrestin

Keywords

SIGNALING PROTEIN

Function / homology

Function and homology information

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 / signal transduction / identical protein binding / membrane / cytosol
Similarity search - Function

Biological species

Bos taurus (cattle)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.097 Å

Authors

Kang, M. / Jang, K. / Eger, B.T. / Ernst, O.P. / Choe, H.W. / Kim, Y.J.

Funding support

Korea, Republic Of, 2items

Citation

Journal: 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

Deposition	Jun 10, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 27, 2021	Provider: repository / Type: Initial release
Revision 1.1	Feb 8, 2023	Group: 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 1.2	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7f1w.cif.gz	580.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7f1w.ent.gz	485.4 KB	Display	PDB format
PDBx/mmJSON format	7f1w.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7f1w_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	7f1w_full_validation.pdf.gz	1.7 MB	Display
Data in XML	7f1w_validation.xml.gz	49.3 KB	Display
Data in CIF	7f1w_validation.cif.gz	66.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f1/7f1w ftp://data.pdbj.org/pub/pdb/validation_reports/f1/7f1w	HTTPS FTP

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Related structure data

Related structure data	7f1xC 7jsmC 7jtbC 7jxaC 7morC 7mp0C 7mp1C 7mp2C 1cf1S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1cf1-2 3ugx-3 3ugx-1 3gd1-1 1cf1-4 7f1w-4 5tv1-d 4zrg-d 3p2d-1 7f1x-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#147 - Mar 2012 Rhodopsin similarity (1) #58 - Oct 2004 G Proteins similarity (1) #100 - Apr 2008 Adrenergic Receptors similarity (1) #27 - Mar 2002 Bacteriorhodopsin similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #66 - Jun 2005 Carotenoid Oxygenase similarity (1) #110 - Feb 2009 Auxin and TIR1 Ubiquitin Ligase similarity (1) #225 - Sep 2018 Phytase similarity (1) #218 - Feb 2018 EPSP Synthase and Weedkillers similarity (1) #88 - Apr 2007 Clathrin similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#147 - Mar 2012
Rhodopsin
similarity (1)
#58 - Oct 2004
G Proteins
similarity (1)
#100 - Apr 2008
Adrenergic Receptors
similarity (1)
#27 - Mar 2002
Bacteriorhodopsin
similarity (1)
#60 - Dec 2004
Ubiquitin
similarity (1)
#66 - Jun 2005
Carotenoid Oxygenase
similarity (1)
#110 - Feb 2009
Auxin and TIR1 Ubiquitin Ligase
similarity (1)
#225 - Sep 2018
Phytase
similarity (1)
#218 - Feb 2018
EPSP Synthase and Weedkillers
similarity (1)
#88 - Apr 2007
Clathrin
similarity (1)

Deposited unit

A: S-arrestin

B: S-arrestin

D: S-arrestin

C: S-arrestin

hetero molecules

183 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: S-arrestin

hetero molecules

defined by author&software
Evidence: native gel electrophoresis
46 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: S-arrestin

hetero molecules

defined by author&software
46 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

D: S-arrestin

hetero molecules

defined by author&software
46 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

C: S-arrestin

defined by author&software
45.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	20
Space group name H-M	C222₁

#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 Mass: 660.035 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₁₈O₂₄P₆ / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 4.2 Å³/Da / Density % sol: 73.7 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 28, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.097→46.195 Å / Num. obs: 55228 / % possible obs: 99 % / Redundancy: 4.6 % / CC_1/2: 0.993 / R_merge(I) obs: 0.075 / R_pim(I) all: 0.04 / Net I/σ(I): 11.6
Reflection shell	Resolution: 3.097→3.208 Å / R_merge(I) obs: 0.417 / Num. unique obs: 5331 / CC_1/2: 0.775 / R_pim(I) all: 0.219 / R_rim(I) all: 0.475

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Processing

Software

Name	Version	Classification
PHENIX	(1.10_2155: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method 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

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2406	2757	4.99 %	RANDON
R_work	0.2153	-	-	-
obs	0.2165	55209	99.21 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 3.097→46.195 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11360	0	108	0	11468

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	11692
X-RAY DIFFRACTION	f_angle_d	0.555	15874
X-RAY DIFFRACTION	f_dihedral_angle_d	9.455	7174
X-RAY DIFFRACTION	f_chiral_restr	0.046	1850
X-RAY DIFFRACTION	f_plane_restr	0.005	1994

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.0972-3.1506	0.3646	132	0.3612	2409	X-RAY DIFFRACTION	94
3.1506-3.2079	0.3314	153	0.31	2636	X-RAY DIFFRACTION	100
3.2079-3.2696	0.3303	143	0.2918	2624	X-RAY DIFFRACTION	100
3.2696-3.3363	0.2846	134	0.2877	2599	X-RAY DIFFRACTION	100
3.3363-3.4088	0.337	122	0.2888	2644	X-RAY DIFFRACTION	100
3.4088-3.4881	0.3063	141	0.2733	2591	X-RAY DIFFRACTION	100
3.4881-3.5753	0.2756	135	0.249	2633	X-RAY DIFFRACTION	100
3.5753-3.6719	0.2738	138	0.2578	2616	X-RAY DIFFRACTION	100
3.6719-3.7799	0.2612	147	0.2409	2602	X-RAY DIFFRACTION	100
3.7799-3.9018	0.2677	148	0.2308	2649	X-RAY DIFFRACTION	100
3.9018-4.0412	0.2566	133	0.2278	2611	X-RAY DIFFRACTION	100
4.0412-4.2029	0.2534	124	0.2167	2656	X-RAY DIFFRACTION	100
4.2029-4.3941	0.1989	142	0.1866	2638	X-RAY DIFFRACTION	100
4.3941-4.6255	0.2118	143	0.1696	2609	X-RAY DIFFRACTION	100
4.6255-4.915	0.1778	144	0.1527	2641	X-RAY DIFFRACTION	100
4.915-5.294	0.1935	140	0.1604	2676	X-RAY DIFFRACTION	100
5.294-5.8258	0.2089	128	0.1853	2658	X-RAY DIFFRACTION	100
5.8258-6.6667	0.2126	137	0.2007	2679	X-RAY DIFFRACTION	100
6.6667-8.3911	0.2147	149	0.1911	2675	X-RAY DIFFRACTION	99
8.3911-46.195	0.2213	124	0.2068	2606	X-RAY DIFFRACTION	93

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	1.4647	1.3866	1.6236	2.2611	1.2111	1.7281	-0.1711	-0.0599	0.1162	-0.2715	-0.0271	0.2262	-1.1155	0.7339	0.0582	0.5811	-0.0532	-0.0616	0.5434	0.1507	0.4372	-26.5417	-19.3288	72.9411
2	2.6726	1.693	0.0709	0.9289	-0.3135	2.6508	0.049	-0.124	0.0503	0.2794	-0.0913	0.1306	-0.486	0.2315	0.0322	0.4081	-0.0159	-0.0054	0.3371	0.0299	0.2919	-29.0917	-27.5813	81.5414
3	0.4651	-0.9452	0.7051	2.8339	-1.3051	1.2345	-0.0221	-0.4586	0.0005	0.3563	0.2417	-0.3315	-0.4196	0.0266	-0.2781	0.2979	-0.0393	0.0431	0.6528	0.0857	0.4412	-27.0301	-32.6449	75.941
4	1.689	0.4255	1.1455	2.7784	-0.4315	3.9134	-0.0436	0.1039	0.4552	-0.0927	-0.0633	-0.0425	-0.305	0.0672	0.047	0.4416	-0.0562	-0.0188	0.5751	0.0807	0.4429	-30.7188	-24.9985	70.9308
5	0.8849	-0.151	0.0324	1.6201	0.2995	2.6643	-0.1004	-0.1721	0.0381	0.3192	-0.0989	0.0267	-0.7855	0.5612	0.3168	0.3865	0.0118	-0.038	0.5435	0.1043	0.4373	-31.2919	-28.1402	72.2802
6	3.087	0.7282	0.5787	3.7312	-0.2202	1.6036	-0.1347	0.5365	0.1662	-0.451	-0.0475	0.0451	-0.422	0.7138	0.1392	0.5312	-0.0529	0.0533	0.3641	0.0855	0.2484	-39.9185	-21.2036	30.6569
7	2.944	-0.6876	0.9235	0.5163	-1.289	3.2464	-0.101	0.1938	0.2491	-0.1089	0.1113	0.026	-0.3506	-0.4489	0.0479	0.5819	-0.0763	0.0507	0.4972	-0.0029	0.4507	-45.0385	-17.6811	33.3983
8	0.6621	-0.0628	0.6402	0.589	-0.4433	2.369	0.0886	-0.0739	-0.2249	0.2271	0.2509	0.2163	-0.7136	-0.3791	-0.2721	0.7993	-0.0197	-0.0052	0.5188	0.0895	0.416	-44.5554	-16.7599	40.6544
9	2.2329	-1.4215	0.3567	3.1063	1.3371	4.1675	-0.3817	0.085	0.2561	0.5208	0.421	-0.0846	0.0873	-0.2766	-0.0191	0.5991	-0.0111	0.095	0.5308	0.1013	0.5349	-39.3854	-23.3285	57.4882
10	0.0719	-0.2438	0.0575	1.4072	-1.3372	1.9696	-0.1568	-0.3478	-0.0856	0.2281	0.0436	0.0666	-0.5443	-0.2456	-0.2701	0.4236	0.0526	0.0583	0.4473	0.0301	0.3456	-50.117	-21.8415	34.7263
11	2.1659	1.619	3.0298	1.0525	1.2663	5.6589	-0.1754	-0.2419	0.3362	-0.0623	-0.1459	-0.0689	-0.8467	-0.2534	0.1792	0.6979	-0.0419	-0.0665	0.5359	0.0699	0.4883	-29.8733	-15.8422	59.5252
12	1.724	-0.5066	-0.1776	3.1642	-0.0214	2.8319	0.1565	0.4336	-0.2095	-0.6003	-0.309	-0.5751	0.2451	0.6864	0.0192	0.5244	0.103	0.1021	0.7208	0.0136	0.5368	-21.7794	-39.231	-12.7386
13	0.65	-0.4157	-0.498	2.0597	0.4687	1.5306	0.0903	0.021	0.0645	0.2409	-0.1057	-0.0894	-0.5318	0.0028	-0.0021	0.585	-0.089	-0.0561	0.4472	0.061	0.3619	-34.1275	-12.7124	7.2145
14	1.1073	-1.6515	-1.9358	3.155	2.0952	3.4182	0.1164	-0.1737	0.3095	-0.0876	0.3974	-0.7841	-0.4233	1.0002	-0.2777	0.623	-0.1728	-0.0221	0.6745	0.0387	0.5459	-26.8031	-16.1687	1.4884
15	4.3592	-0.5572	1.3279	1.491	0.5494	0.9217	0.1311	0.0667	-0.3626	-0.0531	-0.1163	-0.0386	0.0096	0.1407	-0.02	0.362	0.1088	0.012	0.5102	-0.0206	0.2756	25.3324	-50.9905	16.2013
16	4.3055	-0.0484	2.3138	2.6768	-0.8111	1.3717	-0.5701	-0.7275	0.2375	0.4163	0.4685	-0.0029	-0.4085	-0.4409	-0.1568	0.3968	0.207	0.0036	0.59	-0.0476	0.4441	24.2802	-41.7181	15.9754
17	2.1965	0.4943	-0.5282	1.6709	0.117	0.8807	-0.0322	-0.0461	0.19	-0.1505	-0.0123	0.0977	0.0308	-0.0134	0.0071	0.3483	0.0891	-0.0249	0.4713	-0.0016	0.3596	23.1553	-46.7462	12.7645
18	7.9154	0.4839	-1.0252	0.6297	0.6809	1.0426	0.0739	0.149	0.8546	0.0386	0.1735	-0.0244	0.1836	-0.2309	-0.2801	0.4167	0.0369	-0.0752	0.5044	0.0375	0.4411	10.1692	-50.5767	15.9109
19	2.5399	0.3386	1.1898	0.3723	-0.3903	1.1787	-0.0168	-0.1949	-0.391	-0.2278	0.1577	0.1883	0.1884	-0.1784	-0.0989	0.361	0.0197	-0.0819	0.3694	-0.0394	0.4776	-20.7691	-54.3332	7.0957
20	4.9304	0.7496	-0.0899	1.1066	0.3974	0.1396	-0.3167	0.7484	-0.7998	-0.2698	0.1986	-0.0414	0.2555	0.1397	0.1519	0.5554	0.021	-0.1077	0.5946	-0.0506	0.5177	-14.3863	-56.3612	3.3792
21	4.039	-0.3117	1.9867	0.0557	-0.823	0.38	0.2226	0.3816	-0.5286	-0.0467	-0.0705	0.292	0.077	0.1173	-0.1681	0.4749	0.0869	-0.039	0.5264	-0.1007	0.4839	0.1997	-54.3808	7.7693
22	2.0323	-1.4411	-1.5451	2.0081	0.5378	1.7095	-0.2931	-0.299	0.3476	0.8325	-0.1656	1.0912	0.3316	-0.4672	0.2755	0.711	-0.1395	0.2889	0.9016	-0.2522	1.085	-62.3829	-34.6957	34.0474
23	2.6835	0.412	-0.4926	0.1856	-0.4693	0.9142	-0.0515	-0.3699	0.5157	0.225	-0.3053	1.3533	-0.1759	-0.6522	-0.2072	0.5402	-0.0545	0.1807	0.9058	-0.256	1.433	-69.489	-34.1953	28.5225
24	1.2927	0.3667	-0.4032	1.6796	0.5031	2.5135	-0.0262	0.0268	-0.269	0.2721	-0.348	0.572	0.0754	-0.2762	0.1712	0.4016	-0.1769	-0.0021	0.5709	-0.0082	0.7743	-52.1182	-50.1125	20.9974
25	1.795	-0.9339	-0.4886	3.177	1.8972	2.5934	-0.1463	-0.0807	-0.4899	0.6584	0.0314	-0.0724	0.4465	-0.0184	0.1201	0.5216	-0.1525	-0.0086	0.4904	0.1207	0.6393	-42.2176	-60.1898	19.0147
26	1.09	-0.5956	-0.9188	1.9808	-0.0368	0.8535	-0.5313	-0.5574	-0.764	0.1881	0.1947	0.8985	-0.1205	-0.2186	0.3989	0.918	-0.0902	0.4438	1.0464	0.0019	1.1022	-66.238	-49.6481	34.2154

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 9 through 40 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 41 through 67 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 68 through 101 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 102 through 154 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 155 through 188 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 189 through 219 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 220 through 247 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 248 through 286 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 287 through 322 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 323 through 346 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 347 through 385 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 10 through 178 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 179 through 336 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 337 through 385 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 9 through 67 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 68 through 101 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 102 through 165 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 166 through 188 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 189 through 247 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 248 through 280 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 281 through 386 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 11 through 77 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 78 through 130 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 131 through 219 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 220 through 356 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 357 through 384 )

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