PDB-7f1x: X-ray crystal structure of visual arrestin complexed with inosito...

ID or keywords:

Entry

Database: PDB / ID: 7f1x

Title

X-ray crystal structure of visual arrestin complexed with inositol 1,4,5-triphosphate

Components

S-arrestin

Keywords

SIGNALING 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 / phosphoprotein binding / G protein-coupled receptor binding / signal transduction / identical protein binding ...
Similarity search - Function

Biological species

Bos taurus (domestic cattle)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3 Å

Authors

Jang, K. / Kang, M. / Eger, B.T. / Choe, H.W. / Ernst, O.P. / 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	Nov 3, 2021	Group: Derived calculations Category: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop Item: _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value
Revision 1.2	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 1.3	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	7f1x.cif.gz	582.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7f1x.ent.gz	490.2 KB	Display	PDB format
PDBx/mmJSON format	7f1x.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7f1x_validation.pdf.gz	2.5 MB	Display	wwPDB validaton report
Full document	7f1x_full_validation.pdf.gz	2.5 MB	Display
Data in XML	7f1x_validation.xml.gz	49.4 KB	Display
Data in CIF	7f1x_validation.cif.gz	66.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f1/7f1x ftp://data.pdbj.org/pub/pdb/validation_reports/f1/7f1x	HTTPS FTP

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Related structure data

Related structure data	7f1wC 7jsmC 7jtbC 7jxaC 7morC 7mp0C 7mp1C 7mp2C 1cf1S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1cf1-4 1suj-d 1g4r-d 3ugx-3 1zsh-d 1g4m-1 6kl7-1 3gd1-1 7f1w-4 7kga-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)

Deposited unit

A: S-arrestin

B: S-arrestin

C: S-arrestin

D: 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
45.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: S-arrestin

hetero molecules

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

3

C: S-arrestin

hetero molecules

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

4

D: S-arrestin

hetero molecules

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

Unit cell

Length a, b, c (Å)	167.566, 187.702, 190.817
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
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 (domestic cattle) / References: UniProt: P08168
#2: Chemical	ChemComp-I3P / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE Mass: 420.096 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₅O₁₅P₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PTD / PENTANEDIAL Mass: 100.116 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₅H₈O₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂ / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H₂O
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: 4.13 Å³/Da / Density % sol: 70.21 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / 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→47.7 Å / Num. obs: 59857 / % possible obs: 99.2 % / Redundancy: 7.3 % / B_iso Wilson estimate: 71.4 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.075 / R_pim(I) all: 0.03 / Net I/σ(I): 19.8
Reflection shell	Resolution: 3→3.16 Å / R_merge(I) obs: 0.469 / Num. unique obs: 8712 / CC_1/2: 0.918 / R_pim(I) all: 0.183 / R_rim(I) all: 0.504

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Processing

Software

Name	Version	Classification
PHENIX	1.10_2155	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1CF1

1cf1

Resolution: 3→46.925 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.65 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2388	2993	5.02 %	RANDOM
R_work	0.2061	56598	-	-
obs	0.2077	59591	98.8 %	-

Solvent computation

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

Displacement parameters

B_iso max: 216.48 Å² / B_iso mean: 73.3421 Å² / B_iso min: 37.13 Å²

Refinement step

Cycle: final / Resolution: 3→46.925 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11475	0	121	2	11598
B_iso mean	-	-	95.52	44.4	-
Num. residues	-	-	-	-	1453

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	11819
X-RAY DIFFRACTION	f_angle_d	0.56	16030
X-RAY DIFFRACTION	f_chiral_restr	0.045	1873
X-RAY DIFFRACTION	f_plane_restr	0.004	2019
X-RAY DIFFRACTION	f_dihedral_angle_d	11.34	7260

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
3-3.0492	0.3888	136	0.3221	2694	100
3.0492-3.1018	0.3515	145	0.3283	2656	100
3.1018-3.1581	0.3553	148	0.2949	2702	100
3.1581-3.2189	0.3396	132	0.2695	2725	100
3.2189-3.2846	0.3026	160	0.2455	2644	100
3.2846-3.356	0.2462	156	0.2506	2711	100
3.356-3.434	0.2505	149	0.2366	2681	100
3.434-3.5199	0.275	142	0.2388	2675	100
3.5199-3.615	0.2992	134	0.2381	2729	100
3.615-3.7213	0.267	136	0.2264	2693	99
3.7213-3.8414	0.2404	130	0.2266	2688	99
3.8414-3.9786	0.2555	142	0.2113	2726	100
3.9786-4.1378	0.2436	143	0.2044	2675	99
4.1378-4.326	0.213	143	0.1849	2737	99
4.326-4.5539	0.1788	156	0.1682	2681	100
4.5539-4.839	0.1792	138	0.1507	2743	99
4.839-5.2121	0.1985	152	0.1563	2713	100
5.2121-5.7358	0.2167	141	0.1894	2751	100
5.7358-6.5639	0.2572	147	0.1981	2762	100
6.5639-8.2624	0.2349	148	0.191	2764	100
8.2624-46.925	0.2036	115	0.204	2448	84

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	4.7014	2.3935	1.8386	4.0084	-0.7103	3.1024	-0.2636	-0.4327	0.4767	-0.4234	-0.1598	0.2246	-0.3469	-0.5648	0.3584	0.3317	0.1149	0.021	0.4437	0.0363	0.4935	137.4414	244.2288	205.1785
2	7.0853	-1.3087	0.2522	1.8165	0.085	0.9461	0.2545	-1.0113	0.6176	0.0075	-0.1258	-0.0465	0.0827	-0.0426	-0.1545	0.459	-0.0031	0.006	0.5745	0.0465	0.3477	143.1936	237.5871	210.5334
3	4.3718	-0.8604	-2.0974	1.815	0.7785	1.0823	-0.5767	0.4215	-0.1105	0.0656	0.4418	-0.2575	0.2762	-0.2512	0.0761	0.4457	-0.0103	-0.0291	0.5853	0.0494	0.4145	148.4485	228.2047	195.7382
4	2.7399	0.9803	0.0735	0.8156	-0.4013	0.3947	0.1234	-0.4917	-0.3299	0.4799	-0.1258	-0.0508	0.0311	0.1069	0.0454	0.594	0.2009	0.0301	0.6904	0.088	0.523	138.0856	230.0351	213.8039
5	3.2304	0.8212	0.1047	1.3324	0.3873	3.7429	0.1567	-0.8546	0.1743	0.2251	-0.1686	-0.215	-0.1719	-0.1956	-0.0511	0.3758	0.0822	-0.0257	0.4638	0.0254	0.441	144.7498	237.4367	212.2704
6	3.1828	-0.138	0.0888	2.0523	-0.536	1.2662	-0.2843	0.407	0.1545	-0.5358	0.1972	0.1303	0.2754	-0.0217	0.0395	0.6298	0.018	-0.0322	0.6527	0.0364	0.5127	143.5971	229.8397	194.5169
7	5.3741	1.1636	-0.2184	0.8091	-0.1678	0.7238	-0.3767	-0.7739	0.2026	0.0363	0.2811	-0.0261	-0.3197	-0.1214	0.0156	0.5444	0.1525	0.0471	0.6166	0.0148	0.5976	157.1886	237.7318	206.6055
8	3.5299	-0.1395	-0.9213	1.1652	-0.0269	3.6018	-0.3956	-0.9107	0.3722	0.0503	0.3682	-0.0326	0.0614	0.5282	0.0144	0.5	-0.0117	0.0442	0.4645	-0.0091	0.6316	188.8392	240.3573	200.4753
9	5.3442	1.1125	-0.5913	2.1965	-0.0297	0.591	-0.1696	0.4756	0.822	-0.1466	0.1669	-0.1193	-0.1489	-0.1233	-0.0016	0.5404	0.0696	0.0684	0.4335	0.0822	0.5007	182.894	244.417	194.8778
10	3.4637	-0.2817	0.4482	3.2797	-0.7837	3.5882	-0.1943	0.2656	0.0305	0.0617	0.1609	0.0236	-0.2907	-0.207	0.0629	0.4933	0.1352	0.0287	0.6776	0.0659	0.4959	162.5354	238.0277	197.7065
11	0.9503	-0.3806	-0.0093	1.05	0.3352	0.1194	0.187	0.7249	0.2509	-0.0335	-0.0533	-0.5629	-0.2622	-0.2142	-0.0238	0.3467	0.0824	0.055	0.6066	0.0266	0.5543	185.5601	239.3604	189.9352
12	6.505	-1.2499	-2.4237	0.8056	1.2115	1.8442	0.2337	-0.2234	0.852	-0.1706	-0.0369	0.0063	-0.2171	-0.1199	-0.1738	0.6471	0.0641	0.0717	0.5409	0.0159	0.679	158.6382	245.9747	205.6718
13	2.1675	0.223	1.7163	2.5144	0.0448	1.9141	-0.1875	-0.4692	-0.2195	0.6779	-0.1379	-1.172	-0.072	0.6703	0.0712	0.7252	-0.0818	-0.2134	0.9544	0.1428	1.1225	232.4745	222.1372	222.6745
14	1.6178	0.5578	-0.2061	3.4054	-1.2357	3.3401	0.4258	-0.0641	-0.3224	0.5128	-0.657	-0.9477	0.3205	0.4717	0.2949	0.7323	-0.1439	-0.1463	0.8056	-0.0257	0.9701	224.4242	224.8662	219.4178
15	1.8497	-1.1467	0.6972	3.9624	-1.2548	2.1674	0.0023	-0.0625	0.6052	0.3355	-0.1028	-0.2429	-0.4361	0.0613	0.1085	0.621	-0.2048	0.042	0.479	-0.1165	0.7475	210.7595	248.6633	208.7423
16	1.2184	0.8091	1.1282	1.0105	0.0693	4.4709	0.3974	-0.0687	-1.1553	0.0336	-0.3215	0.4906	-0.0364	-0.5721	-0.0906	0.6409	-0.2312	0.1336	0.6581	-0.0333	0.9003	202.3445	252.9694	205.146
17	1.7583	0.3022	0.3831	1.4621	-0.7144	1.6474	-0.1379	-1.1528	0.7843	0.2757	0.1219	-0.864	0.634	0.4633	-0.254	1.0309	-0.1959	-0.2878	1.3096	-0.1414	1.2197	232.6854	237.251	225.7955
18	1.6787	0.7894	-1.4864	2.1075	0.356	3.7475	-0.0285	-0.0013	-0.2702	0.0617	0.0084	0.0643	1.1027	-0.7917	-0.0687	0.7464	-0.1291	0.0182	0.616	-0.1362	0.603	193.7478	206.2874	264.0255
19	2.3312	1.5619	-0.5543	1.5571	0.2398	2.5857	0.0246	0.1546	-0.2508	0.2005	-0.0103	-0.1165	0.386	-0.3437	0.0718	0.5087	-0.0317	-0.1077	0.4073	-0.0018	0.4396	196.4693	214.3591	272.71
20	0.1124	-0.0786	-0.4637	2.5586	-0.28	2.0482	0.2924	-0.0007	-0.0011	0.3108	0.2844	0.2057	0.1136	-0.093	-0.3942	0.3972	-0.0675	-0.054	0.5913	-0.1416	0.5526	195.5731	219.2229	266.8707
21	1.5717	-0.5295	0.3494	1.6396	0.9839	2.6194	0.1445	-0.0029	-0.1317	0.0691	-0.1178	-0.0444	0.2745	-0.175	-0.0412	0.6103	-0.1148	-0.0039	0.5719	-0.07	0.5264	198.6849	214.0492	266.1232
22	1.2722	0.1783	-0.4776	1.0652	0.6051	6.4542	-0.0569	0.2262	-0.2318	-0.0623	0.1047	0.0565	0.4512	0.1913	0.0689	0.6958	-0.0747	0.0475	0.5444	-0.0753	0.5435	197.116	210.5626	252.7631
23	3.6664	-0.284	-1.105	2.283	0.5475	3.7466	0.041	0.3208	0.4432	-0.2252	0.2084	-0.015	0.5706	-0.5918	-0.2155	0.6447	-0.0713	-0.0812	0.409	-0.0878	0.4587	206.9588	208.6818	221.6099
24	0.7268	-0.7451	-0.7984	0.7829	1.1536	4.5426	-0.0205	-0.0569	0.1665	0.0416	0.3793	-0.2253	0.7726	0.7399	-0.2931	0.7129	-0.0476	-0.0181	0.548	-0.0763	0.5355	212.0899	204.8947	227.2425
25	1.0574	0.3118	-0.8987	2.0683	-0.364	4.7727	-0.1192	-0.1297	-0.1185	0.2032	0.0468	0.0093	0.6215	0.3365	0.0723	0.6021	-0.0018	-0.0905	0.5651	-0.0541	0.5315	210.5237	208.9065	239.8077
26	0.9384	0.5631	-1.7948	1.1093	0.4251	6.1933	-0.3627	-0.253	-0.2533	0.1858	-0.2267	0.0606	0.8712	0.1543	0.3689	0.7779	-0.0941	0.0662	0.5611	-0.078	0.5399	197.7412	203.0967	249.9557
27	2.1329	-0.3292	0.6336	3.2159	-0.0589	3.639	0.1785	0.4939	0.2467	-0.5658	-0.1264	0.477	-0.1422	-0.7251	-0.0971	0.5552	0.0873	-0.062	0.7734	0.0596	0.5693	188.9335	227.1296	178.1234
28	0.7891	-0.6315	0.2434	3.3183	-1.375	2.6164	0.01	0.1243	-0.0729	0.0625	-0.0175	0.2121	0.6743	-0.2138	-0.0725	0.7769	-0.1374	0.0525	0.5473	-0.1137	0.4516	199.4384	201.1326	196.7289

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 9 through 26 )	A	9 - 26
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 27 through 55 )	A	27 - 55
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 56 through 83 )	A	56 - 83
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 84 through 101 )	A	84 - 101
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 102 through 132 )	A	102 - 132
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 133 through 165 )	A	133 - 165
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 166 through 188 )	A	166 - 188
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 189 through 219 )	A	189 - 219
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 220 through 286 )	A	220 - 286
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 287 through 322 )	A	287 - 322
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 323 through 346 )	A	323 - 346
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 347 through 386 )	A	347 - 386
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 10 through 132 )	B	10 - 132
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 133 through 190 )	B	133 - 190
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 191 through 336 )	B	191 - 336
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 337 through 356 )	B	337 - 356
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 357 through 385 )	B	357 - 385
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 9 through 40 )	C	9 - 40
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 41 through 67 )	C	41 - 67
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 68 through 101 )	C	68 - 101
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 102 through 165 )	C	102 - 165
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 166 through 188 )	C	166 - 188
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 189 through 219 )	C	189 - 219
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 220 through 280 )	C	220 - 280
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 281 through 346 )	C	281 - 346
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 347 through 385 )	C	347 - 385
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 10 through 178 )	D	10 - 178
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 179 through 385 )	D	179 - 385

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