PDB-6b9m: Crystal structure of UHRF1 TTD domain in complex with the polybas...

ID or keywords:

Entry

Database: PDB / ID: 6b9m

Title

Crystal structure of UHRF1 TTD domain in complex with the polybasic region

Components

(E3 ubiquitin-protein ligase UHRF1) x 2

Keywords

TRANSFERASE /

complex

Function / homology

Function and homology information

: /

: / histone H3 ubiquitin ligase activity / H3K9me3 modified histone binding / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / intestinal epithelial structure maintenance / DNA damage sensor activity / hemi-methylated DNA-binding /

homologous recombination ...
Similarity search - Function

Biological species

Danio rerio (zebrafish)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.68 Å

Authors

Song, J. / Tan, X.

Citation

Journal: Structure / Year: 2018
Title: An Intramolecular Interaction of UHRF1 Reveals Dual Control for Its Histone Association.
Authors: Gao, L. / Tan, X.F. / Zhang, S. / Wu, T. / Zhang, Z.M. / Ai, H.W. / Song, J.

History

Deposition	Oct 10, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 14, 2018	Provider: repository / Type: Initial release
Revision 1.1	Feb 21, 2018	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Mar 13, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6b9m.cif.gz	218.1 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b9/6b9m ftp://data.pdbj.org/pub/pdb/validation_reports/b9/6b9m	HTTPS FTP

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Related structure data

Similar structure data	4mng-1 1m1p-7 6urh-d 4lv5-d 2jix-1 1m5v-1 4mng-2 6ym0-d 5o14-2 6zlr-3 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#116 - Aug 2009 Sulfotransferases similarity (1) #163 - Jul 2013 HIV Capsid similarity (2) #139 - Jul 2011 DNA Methyltransferase similarity (1) #56 - Aug 2004 Caspases similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

Deposited unit

A: E3 ubiquitin-protein ligase UHRF1

B: E3 ubiquitin-protein ligase UHRF1

C: E3 ubiquitin-protein ligase UHRF1

D: E3 ubiquitin-protein ligase UHRF1

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	81.219, 66.142, 120.576
Angle α, β, γ (deg.)	90.00, 104.92, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	E3 ubiquitin-protein ligase UHRF1 / RING-type E3 ubiquitin transferase UHRF1 / Ubiquitin-like PHD and RING finger domain-containing ...RING-type E3 ubiquitin transferase UHRF1 / Ubiquitin-like PHD and RING finger domain-containing protein 1 / Ubiquitin-like-containing PHD and RING finger domains protein 1 Mass: 17778.994 Da / Num. of mol.: 3 / Fragment: unp residues 129-280 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: uhrf1 / Production host: Escherichia coli K-12 (bacteria) References: UniProt: E7EZF3, RING-type E3 ubiquitin transferase
#2: Protein/peptide	E3 ubiquitin-protein ligase UHRF1 / Inverted CCAAT box-binding protein of 90 kDa / Nuclear protein 95 / Nuclear zinc finger protein ...Inverted CCAAT box-binding protein of 90 kDa / Nuclear protein 95 / Nuclear zinc finger protein Np95 / hNp95 / RING finger protein 106 / RING-type E3 ubiquitin transferase UHRF1 / Transcription factor ICBP90 / Ubiquitin-like PHD and RING finger domain-containing protein 1 / hUHRF1 / Ubiquitin-like-containing PHD and RING finger domains protein 1 Mass: 4340.991 Da / Num. of mol.: 1 / Fragment: unp residues 638-678 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UHRF1, ICBP90, NP95, RNF106 / Production host: Escherichia coli K-12 (bacteria) References: UniProt: Q96T88, RING-type E3 ubiquitin transferase
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 535 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	The sample sequence of the proteinused is different from sequence (E7EZF3). The accession of the ...The sample sequence of the proteinused is different from sequence (E7EZF3). The accession of the sequence of our sample in NCBI is NP_998242 which is also from Danio rerio (zebrafish)

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.71 Å³/Da / Density % sol: 54.66 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.1M Succinic acid pH7.0, 15% (v/v) Polyethylene glycol 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97741 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 2, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97741 Å / Relative weight: 1
Reflection	Resolution: 1.68→50 Å / Num. obs: 69241 / % possible obs: 98.4 % / Redundancy: 3 % / Net I/σ(I): 27.1

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.68→28.76 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.82

	R_factor	Num. reflection	% reflection
R_free	0.2066	3416	4.93 %
R_work	0.1821	-	-
obs	0.1834	69239	98.33 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.68→28.76 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3769	0	0	535	4304

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	3868
X-RAY DIFFRACTION	f_angle_d	1.127	5228
X-RAY DIFFRACTION	f_dihedral_angle_d	12.004	1478
X-RAY DIFFRACTION	f_chiral_restr	0.05	531
X-RAY DIFFRACTION	f_plane_restr	0.006	693

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 (%)
1.6801-1.7041	0.2525	120	0.2785	2663	X-RAY DIFFRACTION	95
1.7041-1.7295	0.3125	159	0.2675	2639	X-RAY DIFFRACTION	96
1.7295-1.7566	0.2952	155	0.2509	2687	X-RAY DIFFRACTION	97
1.7566-1.7854	0.2626	117	0.2409	2708	X-RAY DIFFRACTION	97
1.7854-1.8161	0.2708	136	0.231	2678	X-RAY DIFFRACTION	97
1.8161-1.8492	0.2655	159	0.2216	2690	X-RAY DIFFRACTION	97
1.8492-1.8847	0.2558	136	0.2235	2755	X-RAY DIFFRACTION	98
1.8847-1.9232	0.2413	148	0.2152	2679	X-RAY DIFFRACTION	98
1.9232-1.965	0.228	141	0.217	2753	X-RAY DIFFRACTION	99
1.965-2.0107	0.2467	159	0.2038	2759	X-RAY DIFFRACTION	98
2.0107-2.061	0.2498	131	0.2085	2720	X-RAY DIFFRACTION	99
2.061-2.1167	0.2519	118	0.2069	2762	X-RAY DIFFRACTION	99
2.1167-2.1789	0.2395	136	0.2007	2779	X-RAY DIFFRACTION	99
2.1789-2.2492	0.2197	154	0.2056	2722	X-RAY DIFFRACTION	99
2.2492-2.3296	0.2246	154	0.199	2748	X-RAY DIFFRACTION	99
2.3296-2.4228	0.2329	135	0.1994	2765	X-RAY DIFFRACTION	99
2.4228-2.533	0.2221	118	0.2013	2810	X-RAY DIFFRACTION	99
2.533-2.6665	0.252	149	0.2067	2751	X-RAY DIFFRACTION	100
2.6665-2.8334	0.2317	183	0.202	2744	X-RAY DIFFRACTION	100
2.8334-3.0519	0.2294	129	0.1951	2828	X-RAY DIFFRACTION	100
3.0519-3.3586	0.201	139	0.1854	2792	X-RAY DIFFRACTION	100
3.3586-3.8437	0.1906	146	0.164	2796	X-RAY DIFFRACTION	100
3.8437-4.8389	0.1549	132	0.129	2843	X-RAY DIFFRACTION	100
4.8389-28.7641	0.1576	162	0.1562	2752	X-RAY DIFFRACTION	96

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	7.9782	-4.5579	-4.6192	6.0653	4.0971	7.9502	-0.4561	-0.5379	-0.2283	0.8185	0.4085	-0.1084	0.4685	0.0748	0.0777	0.369	0.1464	-0.004	0.2717	0.0168	0.1921	54.649	-23.8323	141.0326
2	8.5733	-7.3067	4.7295	7.7177	-6.5294	6.9366	0.0484	0.4081	0.2916	0.0231	-0.1887	-0.0409	0.2882	0.5026	0.0891	0.2805	0.0371	-0.0483	0.2686	-0.041	0.2078	46.1608	-7.999	140.7463
3	5.3344	-1.0988	-2.9544	5.6071	3.7694	8.1636	-0.2969	0.2896	-0.2913	0.2725	-0.1155	0.3942	0.6832	0.0826	0.4139	0.2338	0.075	-0.0366	0.2098	0.0045	0.1468	47.8455	-17.4615	139.3732
4	3.8703	-0.0372	-2.1474	4.5195	-3.6841	5.0367	0.2478	1.729	0.976	-1.6923	0.8605	0.8089	0.9762	-2.3201	-0.7483	0.6058	0.0324	-0.0143	0.7514	0.211	0.3157	57.3059	-17.1425	122.1433
5	3.1779	-5.3515	-2.5918	8.8892	3.7076	4.7181	-0.1596	-0.1743	-0.1591	0.3218	0.0191	0.1781	0.273	0.274	0.1262	0.2234	0.0458	-0.0001	0.1939	0.0023	0.1506	42.9344	-16.3272	140.2333
6	3.2233	2.4845	2.4198	3.8845	4.2126	5.8302	-0.1298	-0.1136	-0.0921	0.2519	0.1603	-0.4916	0.1254	0.2508	-0.1668	0.3069	0.1119	-0.0523	0.2055	-0.0017	0.2727	53.0605	-9.8182	144.2301
7	1.3996	2.3199	0.9316	4.0945	0.5823	8.7016	-0.1078	0.2578	-0.1363	0.2737	0.2193	-0.5262	-0.1148	0.9736	-0.043	0.2273	0.0679	-0.088	0.2754	-0.0532	0.2618	57.7011	3.7538	150.7252
8	5.8861	-0.352	-1.7875	2.0683	0.6014	2.3186	0.3198	0.657	0.8898	-0.2271	-0.6601	0.8004	-0.0624	-0.8376	0.293	0.3376	0.1047	-0.0497	0.3816	-0.0865	0.4509	40.2268	6.216	150.1584
9	7.4843	5.8821	2.603	7.7512	2.8064	2.5996	-0.146	0.3966	0.0653	-0.2018	0.1636	0.0085	-0.3973	0.1397	0.14	0.2756	0.0524	-0.0313	0.2362	0.0223	0.1946	53.0177	6.272	147.9167
10	5.2926	2.5341	1.3373	8.8144	7.4924	8.2616	0.0426	-0.042	0.1871	-0.1922	0.3326	0.0025	-0.9708	0.2318	-0.1584	0.3208	0.0375	-0.0452	0.1651	0.0268	0.2313	53.4261	12.5949	154.7534
11	5.2114	0.2247	1.3674	8.0686	3.2773	2.1395	-0.4164	0.9771	0.5056	-1.2936	-0.2735	0.2616	-0.0419	-0.6546	0.63	0.574	-0.0636	-0.1213	0.487	0.0304	0.3262	48.4531	6.8967	140.9556
12	4.5491	0.879	-0.6608	3.4265	5.335	9.1663	-0.0686	0.0687	-0.2701	0.4647	0.2338	-0.6564	0.4169	0.4235	-0.1221	0.2773	0.0501	-0.0542	0.2097	-0.0171	0.2559	54.4583	-2.461	151.4417
13	6.0412	-1.8157	-2.4569	5.4292	2.5105	8.7106	0.1135	0.1531	-0.4896	-0.028	-0.2357	0.8865	-0.4219	-0.3781	-0.0264	0.1971	0.0293	0.0252	0.1675	-0.0617	0.3974	23.5197	-9.9678	136.6744
14	3.1891	-2.0338	-1.5115	4.6656	0.3302	4.3205	-0.0012	0.2472	-0.3116	0.055	-0.1668	0.9915	-0.1282	-0.6022	0.0882	0.1709	0.0344	0.0148	0.2348	-0.073	0.3901	21.3271	-5.5808	135.0705
15	6.4876	4.9159	4.038	2.0443	7.0289	4.9899	-0.1037	0.3969	-0.5218	0.7381	0.0493	0.0425	1.1147	0.1724	0.1051	0.477	0.0517	0.1028	0.2691	-0.0154	0.3724	31.2156	-22.631	125.8276
16	4.3984	-1.042	-1.7636	7.9682	3.7078	8.963	-0.1198	0.2522	-0.1626	-0.6476	-0.1973	0.3147	-0.4223	-0.3342	0.3307	0.3274	0.0243	-0.0255	0.3604	-0.1193	0.2207	29.462	-16.7162	114.4197
17	4.5171	-1.0412	-1.7544	1.1686	2.1475	5.7727	-0.0136	0.5798	-0.4176	-0.6722	-0.8943	0.6207	-0.8564	-1.3179	0.7488	0.4086	0.0811	-0.0734	0.4599	-0.217	0.355	26.8308	-17.7292	112.5036
18	4.2463	-5.4714	-5.9066	6.9499	5.8398	8.6093	-0.091	0.285	-0.0857	-0.4984	-0.5286	0.7395	-1.1828	-1.2894	0.4639	0.5181	0.2065	-0.1339	0.6386	-0.2684	0.47	25.9249	-14.9809	110.1751
19	3.4376	0.2383	-1.4716	7.1975	1.001	6.6957	0.0817	0.0722	-0.4178	0.0461	-0.2928	0.5273	0.1534	-0.1367	0.2527	0.2499	-0.0175	0.0304	0.2673	-0.1581	0.3982	29.5909	-19.5111	121.5848
20	8.5988	-0.1807	0.3447	2.9551	-0.9487	3.3119	0.1326	-0.6266	-0.0172	0.481	-0.0819	-0.5642	-0.1601	0.1956	-0.0575	0.3502	-0.0153	-0.1192	0.2793	0.0197	0.2449	70.2964	-0.2227	188.1223
21	8.0826	-2.5476	4.596	5.3503	-0.9822	7.969	-0.0674	-0.6792	-0.256	0.2919	0.109	-0.4097	-0.0414	-0.0631	0.0797	0.3316	-0.0355	-0.0412	0.2586	0.0701	0.2455	69.6233	-2.7895	189.5537
22	6.2845	-0.5258	-2.5097	4.916	4.6946	5.0912	-0.3113	-0.7031	-1.9164	-1.2678	0.5943	-0.6603	-0.2244	0.4016	0.175	0.7999	0.0463	0.068	0.8643	-0.1113	0.8696	81.93	-13.0396	180.1351
23	2.8434	0.9721	1.2071	9.6195	-3.9482	5.1227	0.0448	-0.443	-0.6758	0.564	0.2445	0.1815	0.1184	-0.4142	-0.1441	0.2962	-0.0237	-0.0705	0.3403	0.0801	0.3541	66.5551	-4.7496	188.4899
24	3.6555	-4.6708	3.657	5.882	-4.6479	3.5924	-0.8332	-0.5525	0.487	1.5054	0.6109	-0.4577	-0.5313	-0.066	0.431	0.5503	0.0706	-0.1442	0.366	-0.0184	0.2639	60.2746	13.74	182.875
25	5.2294	-2.0083	0.2494	8.8219	1.9676	6.4327	-0.2067	-0.0428	0.2706	-0.5767	0.1467	0.2757	-0.325	-0.119	-0.1033	0.2041	-0.0449	-0.105	0.2494	0.0281	0.22	55.8358	11.8562	173.4619
26	4.3101	3.9464	4.0714	5.8337	1.2093	6.6454	-0.4387	-0.0637	-0.5875	-0.0618	0.9164	1.0067	-0.0824	-0.0302	-0.4026	0.2407	-0.1155	-0.052	0.5471	0.1771	0.502	45.1018	-0.8844	179.5536
27	8.8223	-1.9873	1.4132	6.4726	-2.3881	2.3191	0.2033	-0.0102	-0.0636	-0.5791	0.2456	0.6693	0.213	-0.3929	-0.4709	0.3051	-0.0368	-0.1076	0.2729	0.0252	0.2227	52.7277	6.6738	172.6381
28	8.3004	-5.0634	0.1218	9.0472	-1.9796	3.6607	-0.0586	0.3446	-0.4881	-0.2899	0.172	1.0142	0.4406	-0.4146	-0.0673	0.3797	-0.0621	-0.124	0.3592	0.0382	0.4005	50.2057	4.3934	170.3031
29	7.5228	-3.7359	6.6516	6.8892	-1.3368	8.5939	-0.1172	-0.2053	-0.1943	0.4169	0.2511	0.135	-0.1593	-0.2992	-0.1642	0.2151	-0.0189	-0.0129	0.184	0.0359	0.1815	57.4505	10.0784	179.7795
30	2.6916	4.616	3.4106	7.6258	5.6786	4.1777	0.2126	-0.9043	0.2922	0.7749	-0.358	0.1007	0.331	-0.8289	0.162	0.3067	0.029	0.0815	0.3835	-0.0485	0.2795	41.2171	-6.1021	149.7697
31	8.8948	-2.1881	0.2137	7.2646	5.1164	3.9502	0.1525	0.5494	-0.111	-0.3624	0.0171	-0.383	0.1439	0.3093	-0.137	0.2576	0.047	0.0256	0.2472	-0.0115	0.2614	37.2704	-13.1852	132.413
32	6.1674	7.367	6.837	9.5552	7.0706	9.2029	0.2973	0.4042	-0.9714	-0.2683	0.0556	-0.8568	-0.2438	0.6205	-0.2377	0.2982	0.0466	0.0514	0.2848	-0.0462	0.3807	35.987	-12.9794	127.1412

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 129 through 141 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 142 through 152 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 153 through 164 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 165 through 172 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 173 through 188 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 189 through 205 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 206 through 219 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 220 through 228 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 229 through 240 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 241 through 251 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 252 through 265 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 266 through 277 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 129 through 152 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 153 through 198 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 199 through 205 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 206 through 228 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 229 through 241 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 242 through 265 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 266 through 277 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 130 through 152 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 153 through 163 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 164 through 173 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 174 through 198 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 199 through 205 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 206 through 219 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 220 through 228 )
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 229 through 240 )
28	X-RAY DIFFRACTION	28	chain 'C' and (resid 241 through 265 )
29	X-RAY DIFFRACTION	29	chain 'C' and (resid 266 through 277 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 648 through 657 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 658 through 662 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 663 through 664 )

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