PDB-3ugx: Crystal Structure of Visual Arrestin

ID or keywords:

Entry

Database: PDB / ID: 3ugx

Title

Crystal Structure of Visual Arrestin

Components

S-arrestin

Keywords

SIGNALING PROTEIN / arrestin fold / signal termination /

GPCR / outer segment

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 ...
Similarity search - Function

Biological species

Bos taurus (cattle)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.649 Å

Authors

Batra-Safferling, R. / Granzin, J.

Citation

Journal: J.Mol.Biol. / Year: 2012
Title: Crystal Structure of p44, a Constitutively Active Splice Variant of Visual Arrestin.
Authors: Granzin, J. / Cousin, A. / Weirauch, M. / Schlesinger, R. / Buldt, G. / Batra-Safferling, R.

History

Deposition	Nov 3, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 8, 2012	Provider: repository / Type: Initial release
Revision 1.1	Feb 15, 2012	Group: Structure summary
Revision 1.2	Mar 21, 2012	Group: Database references
Revision 1.3	Nov 8, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.4	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3ugx.cif.gz	564.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3ugx.ent.gz	466 KB	Display	PDB format
PDBx/mmJSON format	3ugx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ug/3ugx ftp://data.pdbj.org/pub/pdb/validation_reports/ug/3ugx	HTTPS FTP

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Related structure data

Related structure data	3uguC C: citing same article (ref.)
Similar structure data	1cf1-2 4zrg-d 3uo3-d 3uo2-d 1cf1-4 3gd1-1 4d3s-1 3lh8-1 4d3s-3 5tv1-d 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

3uguC

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) #134 - Feb 2011 Integrin similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #194 - Feb 2016 Designer Insulins similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science 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)
#134 - Feb 2011
Integrin
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#194 - Feb 2016
Designer Insulins
similarity (1)
#234 - Jun 2019
MDM2 and Cancer
similarity (1)
#259 - Jul 2021
Designed Proteins and Citizen Science
similarity (1)

Deposited unit

A: S-arrestin

B: S-arrestin

C: S-arrestin

D: S-arrestin

hetero molecules

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

1

A: S-arrestin

hetero molecules

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

2

B: S-arrestin

hetero molecules

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

3

C: S-arrestin

hetero molecules

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

4

D: S-arrestin

hetero molecules

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

Unit cell

Length a, b, c (Å)	168.363, 184.329, 90.404
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

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Protein , 1 types, 4 molecules ABCD

#1: Protein	S-arrestin / 48 kDa protein / Retinal S-antigen / S-AG / Rod photoreceptor arrestin / S-arrestin short form Mass: 46535.078 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: SAG / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P08168

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Non-polymers , 6 types, 212 molecules

#2: Chemical	ChemComp-PTD / PENTANEDIAL / Glutaraldehyde Mass: 100.116 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C₅H₈O₂
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-IMD / IMIDAZOLE / Imidazole Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₅N₂
#6: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.77 Å³/Da / Density % sol: 67.36 % Description: CROSSLINK TRIAL. THE CRYSTAL WAS SOAKED WITH 0.1% PENTANEDIAL AND SUBSEQUENTLY TREATED WITH 2.5 MM IMIDAZOLE
Crystal grow	Temperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 18mM PIPES,0.5M KCL,30% EG, 8% PEG 6000, 18% PEG200, 6% PEG 1000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 294.15K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488 Å
Detector	Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 14, 1997
Radiation	Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.488 Å / Relative weight: 1
Reflection	Resolution: 2.649→33.42 Å / Num. all: 81412 / Num. obs: 81412 / % possible obs: 98.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / B_iso Wilson estimate: 49.8 Å² / R_merge(I) obs: 0.075
Reflection shell	Resolution: 2.65→2.69 Å / Redundancy: 2.3 % / R_merge(I) obs: 0.226 / Mean I/σ(I) obs: 4 / Num. unique all: 2958 / % possible all: 73.8

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Processing

Software

Name	Version	Classification
MAR345		data collection
MOLREP		phasing
PHENIX	(phenix.refine: 1.7.1_743)	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.649→32.886 Å / SU ML: 1.03 / σ(F): 0 / Phase error: 24.6 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2534	4080	5.02 %	RANDOM, in thin shells
R_work	0.2086	-	-	-
all	0.2108	81412	-	-
obs	0.2108	81330	98.57 %	-

Solvent computation

Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 37.81 Å² / k_sol: 0.336 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	6.2313 Å²	0 Å²	-0 Å²
2-	-	7.6267 Å²	-0 Å²
3-	-	-	-13.858 Å²

Refinement step

Cycle: LAST / Resolution: 2.649→32.886 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10893	0	144	185	11222

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	11236
X-RAY DIFFRACTION	f_angle_d	1.172	15238
X-RAY DIFFRACTION	f_dihedral_angle_d	18.092	4107
X-RAY DIFFRACTION	f_chiral_restr	0.078	1819
X-RAY DIFFRACTION	f_plane_restr	0.007	1932

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 (%)
2.6486-2.6798	0.3626	100	0.3234	1925	X-RAY DIFFRACTION	72
2.6798-2.7124	0.3643	125	0.2976	2616	X-RAY DIFFRACTION	97
2.7124-2.7468	0.3229	165	0.291	2649	X-RAY DIFFRACTION	100
2.7468-2.7829	0.4137	134	0.3304	2628	X-RAY DIFFRACTION	100
2.7829-2.821	0.3961	140	0.324	2699	X-RAY DIFFRACTION	100
2.821-2.8613	0.3733	149	0.2926	2638	X-RAY DIFFRACTION	100
2.8613-2.9039	0.3416	128	0.277	2721	X-RAY DIFFRACTION	100
2.9039-2.9493	0.2979	136	0.2614	2650	X-RAY DIFFRACTION	100
2.9493-2.9976	0.2887	147	0.2295	2664	X-RAY DIFFRACTION	100
2.9976-3.0493	0.2402	148	0.2341	2686	X-RAY DIFFRACTION	100
3.0493-3.1047	0.2804	129	0.2217	2680	X-RAY DIFFRACTION	100
3.1047-3.1643	0.2456	163	0.2227	2646	X-RAY DIFFRACTION	100
3.1643-3.2289	0.2615	143	0.2084	2686	X-RAY DIFFRACTION	100
3.2289-3.299	0.2907	149	0.2124	2667	X-RAY DIFFRACTION	100
3.299-3.3757	0.2578	166	0.216	2669	X-RAY DIFFRACTION	100
3.3757-3.46	0.2406	123	0.2018	2712	X-RAY DIFFRACTION	100
3.46-3.5535	0.2529	146	0.2045	2669	X-RAY DIFFRACTION	100
3.5535-3.6579	0.2497	132	0.209	2708	X-RAY DIFFRACTION	100
3.6579-3.7758	0.2551	131	0.206	2696	X-RAY DIFFRACTION	100
3.7758-3.9106	0.259	148	0.2021	2707	X-RAY DIFFRACTION	100
3.9106-4.0669	0.2383	136	0.1933	2688	X-RAY DIFFRACTION	100
4.0669-4.2516	0.2439	132	0.1907	2697	X-RAY DIFFRACTION	100
4.2516-4.4752	0.2137	147	0.169	2721	X-RAY DIFFRACTION	100
4.4752-4.7548	0.1859	164	0.1416	2689	X-RAY DIFFRACTION	99
4.7548-5.1207	0.1597	129	0.1465	2724	X-RAY DIFFRACTION	99
5.1207-5.6337	0.2404	136	0.1918	2732	X-RAY DIFFRACTION	99
5.6337-6.4436	0.2924	140	0.2483	2737	X-RAY DIFFRACTION	99
6.4436-8.0981	0.2536	144	0.2184	2730	X-RAY DIFFRACTION	98
8.0981-32.8886	0.2458	150	0.2072	2816	X-RAY DIFFRACTION	97

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	1.0574	-0.406	-0.3935	0.552	-0.0357	0.585	0.0284	0.1762	-0.1195	-0.1318	-0.0444	0.1361	0.0226	0.0476	-0.1436	-0.2809	0.1119	-0.0411	0.169	0.0194	0.3404	110.7874	27.9438	-5.5699
2	0.8148	0.4614	0.4375	0.3143	-0.1307	2.7212	-0.068	0.1347	0.6962	-0.0446	-0.0471	-0.2209	-0.4385	-0.2271	-0.2856	0.0576	-0.0383	0.0868	0.1566	0.1052	0.5286	105.3102	41.5178	4.9897
3	1.9699	-0.1384	-0.0587	0.4014	-0.026	0.4934	0.0853	-0.0268	-0.2471	-0.2341	-0.0928	0.2007	-0.0715	0.0463	-0.0325	-0.4195	-0.0076	0.1444	0.1234	0.0472	0.2892	105.5237	31.5478	1.6615
4	2.5277	0.2271	-0.0781	1.2326	0.676	0.9554	-0.102	0.3057	-0.7051	0.0915	-0.2025	0.0507	0.0254	-0.149	-0.096	0.1624	0.0437	-0.0072	0.2346	0.0736	0.2038	63.0817	36.9729	-3.6729
5	3.3785	-0.2968	0.6881	0.1102	0.1384	0.5464	-0.0515	0.2326	0.4148	-0.0949	-0.081	-0.1887	-0.1344	-0.0142	-0.0157	0.1698	0.0094	0.0518	0.2225	0.0472	0.328	74.2963	42.3848	-5.309
6	0.7179	0.2155	0.1555	0.5335	-0.0635	0.3532	0.0802	0.4972	-0.4762	-0.1841	-0.0551	-0.3476	0.0677	0.2728	0.0747	0.0613	0.1832	-0.0171	0.5258	0.046	0.4365	92.3188	30.1761	-9.9845
7	2.0342	0.4773	-0.5465	1.1624	-0.5985	2.1977	-0.0072	-0.1429	-0.315	0.0087	0.3403	0.399	0.5371	-1.097	0.2312	0.294	-0.1605	-0.0457	0.5685	0.1381	0.3393	22.7503	19.3893	9.6675
8	1.4797	0.3132	-0.5433	1.1637	-0.8626	2.9313	-0.1339	0.1102	-0.2245	-0.2231	0.0756	0.0876	0.5151	-0.1745	-0.0271	0.3135	-0.0148	-0.0678	0.1847	-0.0865	0.1702	38.8098	27.241	-11.1149
9	1.356	-1.2708	0.1193	1.5166	0.0741	0.7976	-0.0472	-0.4679	0.0541	0.6555	-0.0035	-0.277	0.1257	-0.2013	-0.0077	0.3713	0.0384	-0.0371	0.3393	-0.0426	0.3278	56.6867	-25.6518	28.2953
10	0.6186	0.3254	-0.3725	2.3124	1.0068	2.3968	0.0393	-0.1871	0.194	0.135	-0.0512	-0.3859	-0.0316	0.1871	0.0093	0.1201	-0.0239	-0.07	0.1547	-0.0163	0.2748	55.8238	-27.466	19.7361
11	0.294	-1.0312	-0.1815	4.1265	1.0437	0.4546	-0.048	0.0304	-0.1374	0.5406	-0.0757	0.2177	0.0658	-0.0642	-0.0319	0.1874	-0.0002	0.0169	0.1599	-0.0171	0.1704	42.2078	-0.7854	26.843
12	0.1162	-0.3833	-0.3005	2.1119	0.8841	2.1222	0.1256	-0.1859	-0.1541	0.15	-0.09	-0.1269	0.3348	0.0752	0.0233	0.2531	-0.0486	-0.0597	0.2349	-0.0132	0.3389	46.2068	-2.8074	26.8444
13	1.5138	0.2467	-0.5404	1.0696	0.7731	2.3067	0.4096	0.0914	0.5179	-0.4321	0.3821	-0.6086	-1.2317	0.868	0.8879	0.5332	-0.3818	0.2178	0.2293	-0.023	0.4781	62.2233	59.6057	10.517
14	0.4752	0.3458	-0.8471	1.6247	-1.0721	3.1913	0.1224	-0.1599	0.08	0.3649	-0.0273	-0.1905	-0.2011	0.4793	0.0343	0.1625	0.0348	-0.0949	0.2381	-0.0521	0.1823	51.4201	42.8036	33.7623

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 9:55)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 56:78)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 79:188)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 189:219)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 220:346)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 347:386)
7	X-RAY DIFFRACTION	7	chain 'B' and (resseq 11:200)
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 201:385)
9	X-RAY DIFFRACTION	9	chain 'C' and (resseq 9:47)
10	X-RAY DIFFRACTION	10	chain 'C' and (resseq 48:132)
11	X-RAY DIFFRACTION	11	chain 'C' and (resseq 133:306)
12	X-RAY DIFFRACTION	12	chain 'C' and (resseq 307:386)
13	X-RAY DIFFRACTION	13	chain 'D' and (resseq 9:165)
14	X-RAY DIFFRACTION	14	chain 'D' and (resseq 166:385)

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