PDB-5igo: WD40 domain of Arabidopsis thaliana E3 Ubiquitin Ligase COP1 in c...

ID or keywords:

Entry

Database: PDB / ID: 5igo

Title

WD40 domain of Arabidopsis thaliana E3 Ubiquitin Ligase COP1 in complex with peptide from Trib1

Components

E3 ubiquitin-protein ligase COP1
Tribbles homolog 1

Keywords

Hydrolase/Peptide / WD40 domain E3 ligase / Hydrolase-Peptide Complex

Function / homology

Function and homology information

ubiquitin-protein transferase regulator activity / positive regulation of eosinophil differentiation / anthocyanin-containing compound metabolic process /

shade avoidance / positive regulation of flavonoid biosynthetic process / skotomorphogenesis /

photoperiodism, flowering / red, far-red light phototransduction /

photomorphogenesis / negative regulation of smooth muscle cell migration ...
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Uljon, S. / Blacklow, S.C.

Citation

Journal: Structure / Year: 2016
Title: Structural Basis for Substrate Selectivity of the E3 Ligase COP1.
Authors: Uljon, S. / Xu, X. / Durzynska, I. / Stein, S. / Adelmant, G. / Marto, J.A. / Pear, W.S. / Blacklow, S.C.

History

Deposition	Feb 28, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 20, 2016	Provider: repository / Type: Initial release
Revision 1.1	May 11, 2016	Group: Database references
Revision 1.2	Jul 20, 2016	Group: Data collection
Revision 1.3	Nov 22, 2017	Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4	Sep 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5igo.cif.gz	544.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5igo.ent.gz	447.4 KB	Display	PDB format
PDBx/mmJSON format	5igo.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/ig/5igo ftp://data.pdbj.org/pub/pdb/validation_reports/ig/5igo	HTTPS FTP

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Related structure data

Related structure data	5hqgSC 5igqC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3pb4-d 2fgb-d 5ynv-1 3r6i-d 3pb6-d 5hos-d 7coz-2 5jna-1 4uda-d 2uyo-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

5hqgSC

5igqC

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	#75 - Mar 2006 Tissue Factor similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #61 - Jan 2005 Phenylalanine Hydroxylase similarity (1) #163 - Jul 2013 HIV Capsid similarity (2) #56 - Aug 2004 Caspases similarity (1)

Deposited unit

A: E3 ubiquitin-protein ligase COP1

U: Tribbles homolog 1

B: E3 ubiquitin-protein ligase COP1

V: Tribbles homolog 1

C: E3 ubiquitin-protein ligase COP1

W: Tribbles homolog 1

D: E3 ubiquitin-protein ligase COP1

X: Tribbles homolog 1

156 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: E3 ubiquitin-protein ligase COP1

U: Tribbles homolog 1

defined by author&software
39.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: E3 ubiquitin-protein ligase COP1

V: Tribbles homolog 1

defined by author&software
39.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: E3 ubiquitin-protein ligase COP1

W: Tribbles homolog 1

defined by author&software
39.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: E3 ubiquitin-protein ligase COP1

X: Tribbles homolog 1

defined by author&software
39.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	78.516, 87.469, 94.610
Angle α, β, γ (deg.)	90.00, 92.55, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	E3 ubiquitin-protein ligase COP1 / Constitutive photomorphogenesis protein 1 Mass: 38165.688 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: COP1, At2g32950, T21L14.11 / Production host: Trichoplusia ni (cabbage looper) References: UniProt: P43254, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide	Tribbles homolog 1 / TRB-1 / G-protein-coupled receptor-induced gene 2 protein / GIG-2 / SKIP1 Mass: 950.001 Da / Num. of mol.: 4 / Fragment: UNP residues 188-195 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96RU8
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1256 / 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: 2.07 Å³/Da / Density % sol: 40.7 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris 8.5, 16% PEG3350, 2% Tacsimate 8.0.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97931 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 17, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97931 Å / Relative weight: 1
Reflection	Resolution: 1.597→78.438 Å / Num. obs: 167321 / % possible obs: 99 % / Redundancy: 3.4 % / Net I/σ(I): 9
Reflection shell	Resolution: 1.597→1.6 Å / Redundancy: 3.3 % / R_merge(I) obs: 1.16 / Mean I/σ(I) obs: 0.92 / % possible all: 94

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Processing

Software

Name	Version	Classification
PHENIX	1.10_2155	refinement
XDS		data scaling
Aimless		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5HQG

5hqg

Resolution: 1.6→64.2 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.19

	R_factor	Num. reflection	% reflection
R_free	0.2134	8671	5.19 %
R_work	0.1894	-	-
obs	0.1907	166919	98.42 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.6→64.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10300	0	0	1256	11556

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	10555
X-RAY DIFFRACTION	f_angle_d	1	14339
X-RAY DIFFRACTION	f_dihedral_angle_d	13.762	6293
X-RAY DIFFRACTION	f_chiral_restr	0.065	1615
X-RAY DIFFRACTION	f_plane_restr	0.006	1840

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 (%)
1.5958-1.6139	0.398	222	0.4127	4347	X-RAY DIFFRACTION	81
1.6139-1.6329	0.4486	291	0.4393	5330	X-RAY DIFFRACTION	99
1.6329-1.6528	0.4333	296	0.4133	5266	X-RAY DIFFRACTION	99
1.6528-1.6737	0.4326	262	0.3986	5267	X-RAY DIFFRACTION	99
1.6737-1.6958	0.3784	246	0.3615	5369	X-RAY DIFFRACTION	99
1.6958-1.719	0.3676	252	0.3356	5297	X-RAY DIFFRACTION	99
1.719-1.7435	0.353	285	0.302	5287	X-RAY DIFFRACTION	99
1.7435-1.7696	0.2895	241	0.2738	5275	X-RAY DIFFRACTION	99
1.7696-1.7972	0.2755	288	0.246	5252	X-RAY DIFFRACTION	98
1.7972-1.8267	0.262	283	0.2285	5220	X-RAY DIFFRACTION	97
1.8267-1.8582	0.2377	301	0.2209	5312	X-RAY DIFFRACTION	100
1.8582-1.892	0.2386	281	0.2196	5314	X-RAY DIFFRACTION	100
1.892-1.9284	0.242	283	0.2169	5371	X-RAY DIFFRACTION	100
1.9284-1.9677	0.2713	302	0.2145	5263	X-RAY DIFFRACTION	99
1.9677-2.0105	0.228	269	0.2019	5324	X-RAY DIFFRACTION	99
2.0105-2.0573	0.2239	257	0.1713	5315	X-RAY DIFFRACTION	99
2.0573-2.1088	0.1917	268	0.1786	5345	X-RAY DIFFRACTION	99
2.1088-2.1658	0.2189	323	0.1727	5198	X-RAY DIFFRACTION	98
2.1658-2.2295	0.1953	335	0.1713	5262	X-RAY DIFFRACTION	99
2.2295-2.3015	0.2081	310	0.1766	5355	X-RAY DIFFRACTION	100
2.3015-2.3837	0.2151	308	0.1808	5293	X-RAY DIFFRACTION	100
2.3837-2.4792	0.2171	287	0.1712	5324	X-RAY DIFFRACTION	100
2.4792-2.592	0.2096	296	0.1749	5338	X-RAY DIFFRACTION	99
2.592-2.7287	0.2152	313	0.1749	5309	X-RAY DIFFRACTION	99
2.7287-2.8997	0.2037	291	0.1692	5285	X-RAY DIFFRACTION	99
2.8997-3.1236	0.2013	347	0.1664	5328	X-RAY DIFFRACTION	100
3.1236-3.4379	0.1741	315	0.154	5327	X-RAY DIFFRACTION	100
3.4379-3.9353	0.1671	296	0.1569	5369	X-RAY DIFFRACTION	99
3.9353-4.958	0.1566	337	0.1419	5312	X-RAY DIFFRACTION	99
4.958-78.533	0.2034	286	0.1875	5394	X-RAY DIFFRACTION	98

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	1.824	-0.5071	0.1355	2.4488	-0.3528	1.7855	0.042	0.0984	-0.0022	-0.2568	-0.0908	0.1298	-0.0889	-0.097	0.052	0.1804	0.0109	-0.0342	0.1226	-0.0156	0.1553	-4.66	71.6668	44.986
2	2.9341	0.7466	0.3061	2.5884	0.1804	1.6777	-0.1492	0.439	0.2457	-0.1881	0.0243	0.2195	-0.4585	-0.2491	0.0943	0.2775	0.051	-0.0025	0.2821	0.0081	0.2333	-7.4211	78.3199	47.4998
3	1.4564	-0.4066	0.4214	2.1818	-0.2962	2.1238	-0.0901	-0.1784	0.1409	0.3654	0.001	-0.1072	-0.3104	-0.0333	0.0854	0.238	0.0007	-0.0318	0.1515	-0.0133	0.1867	0.5126	72.1969	61.8635
4	0.6254	0.1703	-0.1007	2.3245	-0.922	2.0947	0.0187	-0.0362	0.0526	0.2471	-0.0962	-0.1237	0.0756	0.0812	0.0559	0.1681	0.0005	-0.0259	0.1464	0.0027	0.1539	3.3209	56.511	64.8752
5	0.2838	0.005	0.3285	2.5895	-0.5122	1.6763	0.0792	-0.0227	0.0028	-0.3745	-0.1012	0.0936	0.3934	-0.057	0.0192	0.2561	0.0098	-0.0086	0.1495	0.0008	0.1606	-1.8598	52.8804	45.5312
6	4.0166	1.2953	-1.445	2.5295	-1.0374	3.3934	0.0909	0.4285	0.2353	-0.5914	-0.0226	0.1112	0.1639	-0.1436	0.0057	0.2804	0.0398	-0.0036	0.1887	0.0379	0.1966	-1.0234	64.884	40.4944
7	2.5073	0.1111	0.252	3.322	-0.4192	2.1274	0.0214	-0.1232	-0.1001	-0.4432	-0.1527	0.3784	0.1219	-0.1048	0.0821	0.1924	0.0157	-0.0354	0.1589	-0.0122	0.1769	-6.3605	66.3633	41.011
8	1.8954	-0.9362	0.7465	2.7855	-0.5543	2.2443	0.28	0.2039	0.1532	0.0054	-0.2774	-0.6262	0.0667	0.5035	0.0597	0.1566	0.0461	0.0167	0.2726	0.0696	0.3279	14.1425	60.7055	50.4728
9	1.0194	0.2113	0.2751	2.0267	0.3678	1.2092	-0.0459	0.0555	0.011	-0.0281	0.0055	-0.1007	-0.1518	0.1439	0.0311	0.1438	-0.0121	-0.0144	0.1753	0.0088	0.1693	39.355	71.6607	95.6876
10	0.6624	0.2521	-0.7339	2.4666	0.8527	1.9441	-0.0056	-0.1567	-0.0812	0.0557	0.1552	-0.1866	-0.0223	0.4749	-0.1451	0.1844	0.0126	-0.0134	0.215	-0.0205	0.2206	39.5815	78.835	94.632
11	1.1714	0.2885	0.1126	1.7651	0.6768	1.9808	-0.1038	0.1207	0.0643	-0.4807	0.0414	0.1377	-0.267	0.0457	0.0354	0.286	0.0002	-0.0628	0.1595	0.0123	0.1732	31.138	67.8564	77.0461
12	0.5395	0.0814	-0.1044	1.6491	0.4634	1.6979	-0.0168	0.0581	-0.0055	-0.1726	-0.069	0.1319	0.0978	-0.004	0.0787	0.1766	0.0109	-0.0249	0.153	-0.0055	0.1607	30.3332	50.5598	82.0139
13	0.1822	0.1726	0.3626	2.0705	0.3997	1.7156	0.0164	-0.0122	-0.0455	0.1986	-0.0404	-0.1145	0.1801	0.0726	0.0099	0.1723	0.0032	-0.0048	0.1602	0.0009	0.171	34.8255	52.9886	98.5365
14	2.9835	-0.2976	0.3441	2.6388	0.2894	1.4926	-0.0283	-0.0174	-0.2045	0.2054	-0.0194	-0.1536	0.1494	0.0482	0.0685	0.1591	-0.0124	-0.0132	0.1255	0.0205	0.1411	37.3313	63.8472	100.4081
15	1.5196	0.9655	0.8998	1.5681	0.5294	2.2936	0.0904	0.1727	0.3549	0.1348	-0.1524	0.7472	0.0675	-0.4698	0.0638	0.169	-0.0144	-0.0019	0.2646	-0.0402	0.3104	18.8012	60.6289	91.4038
16	0.8247	-0.3736	-0.2742	2.553	-0.0561	1.6821	-0.0355	-0.0077	-0.0087	-0.1111	0.0913	-0.1801	0.1451	0.1413	-0.0381	0.1635	0.0011	0.0037	0.1671	-0.0216	0.2068	0.4809	43.977	93.5653
17	1.5458	-0.8863	-0.4521	2.52	0.2689	2.1353	-0.2011	-0.2348	-0.1548	0.5109	0.2106	0.1985	0.2256	-0.0551	0.004	0.2319	0.0353	0.0293	0.1851	0.0412	0.2059	-7.6563	44.8347	109.039
18	0.5434	-0.0924	-0.325	1.7412	0.3093	1.517	-0.0376	-0.0431	-0.0504	0.2064	0.0716	0.1225	-0.0867	-0.0488	-0.0331	0.1335	0.027	0.0074	0.1597	0.0128	0.1652	-9.1654	62.8209	105.7854
19	0.4207	-0.4749	-0.421	2.8143	0.1479	1.5928	0.0103	-0.025	-0.0015	-0.3849	0.0285	-0.2407	-0.0896	-0.0522	-0.0072	0.1704	-0.0224	0.0141	0.1564	-0.0224	0.1778	-1.7194	55.7868	87.0083
20	1.6677	-2.1087	-1.2627	2.6604	1.4504	2.325	0.2175	0.1566	0.1492	0.0554	-0.351	0.6556	-0.048	-0.446	0.0914	0.1102	0.0151	0.027	0.295	0.0014	0.3923	-20.6508	56.1557	96.48
21	1.4134	0.6719	-0.442	1.8945	-0.6504	1.172	-0.0543	0.0642	0.0513	0.065	0.0469	0.0826	0.0717	-0.0767	0.0387	0.2233	-0.0009	-0.0076	0.15	-0.0031	0.1589	32.1753	44.8231	48.5301
22	0.5244	-0.0761	0.2277	2.0713	-0.32	1.6869	-0.2984	0.0914	0.0426	-0.0625	0.2277	0.1424	0.3248	-0.3318	0.0287	0.3756	0.0232	-0.038	0.2044	0.0131	0.2459	33.2167	36.5613	46.1572
23	1.6415	0.6855	-0.4344	2.1174	-0.1458	2.263	-0.1189	0.1932	-0.1715	-0.3645	0.0573	-0.1495	0.5046	-0.0336	0.0389	0.3431	-0.019	0.0139	0.1768	-0.0137	0.1944	40.8384	43.849	32.8507
24	2.769	0.0434	0.5571	2.1149	-0.941	2.3603	-0.0908	0.2261	0.0339	-0.4718	-0.0193	-0.2739	0.3558	0.1458	0.1125	0.308	0.0021	0.0511	0.1973	-0.0029	0.2128	45.4056	53.2141	26.5845
25	0.4231	0.0595	-0.2426	1.4931	-0.6981	1.5101	0.0327	0.0141	0.012	0.1398	0.0045	-0.0146	-0.1803	0.0501	-0.0218	0.2056	-0.013	-0.0211	0.1514	0.0027	0.1411	41.5276	64.6739	39.3627
26	0.7086	0.6411	-0.713	2.5561	-0.2698	1.274	0.023	0.0029	0.0338	0.4424	-0.0317	0.1925	-0.2029	0.0676	-0.0056	0.3001	0.0092	0.0009	0.1437	0.0024	0.1562	34.4388	54.8194	54.8944
27	1.9866	1.8384	-1.6902	2.8828	-0.0368	3.3889	0.1442	-0.0956	-0.0483	0.414	-0.1397	-0.6636	0.2563	0.6475	-0.1054	0.1667	-0.0227	-0.0665	0.2824	0.0561	0.3297	53.2771	54.9711	45.7331

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 354 through 393 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 394 through 422 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 423 through 471 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 472 through 557 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 558 through 636 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 637 through 657 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 658 through 674 )
8	X-RAY DIFFRACTION	8	chain 'U' and (resid 354 through 361 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 354 through 404 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 405 through 422 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 423 through 507 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 508 through 576 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 577 through 636 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 637 through 675 )
15	X-RAY DIFFRACTION	15	chain 'V' and (resid 354 through 361 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 352 through 422 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 423 through 471 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 472 through 612 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 613 through 675 )
20	X-RAY DIFFRACTION	20	chain 'W' and (resid 354 through 361 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 352 through 404 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 405 through 422 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 423 through 471 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 472 through 507 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 508 through 612 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 613 through 675 )
27	X-RAY DIFFRACTION	27	chain 'X' and (resid 354 through 361 )

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