PDB-3oln: Crystal structure of the SRA domain of E3 ubiquitin-protein ligas...

ID or keywords:

Entry

Database: PDB / ID: 3oln

Title

Crystal structure of the SRA domain of E3 ubiquitin-protein ligase UHRF2

Components

E3 ubiquitin-protein ligase UHRF2

Keywords

LIGASE / DNA-BINDING / METAL-BINDING / NUCLEUS / PHOSPHORYLATION / TRANSCRIPTION / TRANSCRIPTION REGULATION / UBL CONJUGATION PATHWAY / ZINC-FINGER / STRUCTURAL GENOMICS CONSORTIUM / SGC / PHOSPHOPROTEIN / All beta proteins

Function / homology

Function and homology information

SUMO transferase activity / negative regulation of gene expression via chromosomal CpG island methylation / protein sumoylation / heterochromatin / pericentric heterochromatin / protein autoubiquitination / SUMOylation of transcription cofactors / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

molecular replacement / Resolution: 2.3 Å

Authors

Walker, J.R. / Xue, S. / Avvakumov, G.V. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)

Citation

Journal: To be Published
Title: The Set and Ring Associated (SRA) domain of human ubiquitin-like containing PHD and RING finger domains 2 (UHRF2)
Authors: Walker, J.R. / Xue, S. / Avvakumov, G.V. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)

History

Deposition	Aug 26, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 13, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Sep 6, 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 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3oln.cif.gz	162.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3oln.ent.gz	129.6 KB	Display	PDB format
PDBx/mmJSON format	3oln.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Related structure data	3clzS 1wy8 1z6u 2e6s S: Starting model for refinement
Similar structure data	4tlf-1 1lu1-d 3hmz-d 3ign-d 5u3e-d 3a6r-1 4f21-2 6h35-1 6fs9-d 4m9q-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
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) #56 - Aug 2004 Caspases similarity (1)

Deposited unit

A: E3 ubiquitin-protein ligase UHRF2

B: E3 ubiquitin-protein ligase UHRF2

51.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: E3 ubiquitin-protein ligase UHRF2

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

2

B: E3 ubiquitin-protein ligase UHRF2

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

Unit cell

Length a, b, c (Å)	38.528, 46.259, 58.307
Angle α, β, γ (deg.)	104.55, 93.87, 90.08
Int Tables number	1
Space group name H-M	P1

#1: Protein	E3 ubiquitin-protein ligase UHRF2 / Ubiquitin-like PHD and RING finger domain-containing protein 2 / Ubiquitin-like-containing PHD and ...Ubiquitin-like PHD and RING finger domain-containing protein 2 / Ubiquitin-like-containing PHD and RING finger domains protein 2 / Np95/ICBP90-like RING finger protein / Np95-like RING finger protein / Nuclear zinc finger protein Np97 / Nuclear protein 97 / RING finger protein 107 Mass: 25636.799 Da / Num. of mol.: 2 / Fragment: SRA Domain (UNP residues 419-648) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NIRF, RNF107, RNF107;, UHRF2 / Plasmid: PET28A-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q96PU4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

E3 ubiquitin-protein ligase UHRF2 / Ubiquitin-like PHD and RING finger domain-containing protein 2 / Ubiquitin-like-containing PHD and ...

Mass: 25636.799 Da / Num. of mol.: 2 / Fragment: SRA Domain (UNP residues 419-648)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: NIRF, RNF107, RNF107;, UHRF2 / Plasmid: PET28A-LIC / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q96PU4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 1.96 Å³/Da / Density % sol: 37.15 %
Crystal grow	Temperature: 291 K / pH: 7 Details: 23% PEG3350, 0.1 M HEPES-Na, 5% MPD, 0.2 M NaCl, 1 mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178
Detector	Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 3, 2010
Radiation	Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54178 Å / Relative weight: 1
Reflection	Resolution: 2.3→20 Å / Num. obs: 16102 / % possible obs: 93 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / R_sym value: 0.061 / Net I/σ(I): 24.5256
Reflection shell	Resolution: 2.3→2.34 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3.73 / R_sym value: 0.268 / % possible all: 68.4

-
Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
REFMAC	5.5.0109	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

molecular replacement
Starting model: 3CLZ

3clz

Resolution: 2.3→19.73 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.925 / SU B: 15.46 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.426 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23387	814	5.1 %	RANDOM
R_work	0.18432	-	-	-
obs	0.18682	15216	92.97 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 37.908 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.87 Å²	-0.38 Å²	0.26 Å²
2-	-	0.59 Å²	0.49 Å²
3-	-	-	2.56 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→19.73 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2848	0	0	138	2986

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.021	2936
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.079	1.939	3981
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.159	5	364
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	27.57	21.915	141
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.657	15	449
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.191	15	34
X-RAY DIFFRACTION	r_chiral_restr	0.079	0.2	404
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	2320
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.285	1.5	1813
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.537	2	2902
X-RAY DIFFRACTION	r_scbond_it	0.876	3	1123
X-RAY DIFFRACTION	r_scangle_it	1.478	4.5	1079
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.3→2.359 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.38	31	-
R_work	0.258	835	-
obs	-	-	69.84 %

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	2.4307	7.5681	-3.6019	34.1126	-4.4448	10.0502	0.3238	-0.3596	-0.0362	0.3536	-0.7811	0.0133	-0.7005	0.5378	0.4572	0.2268	-0.1329	-0.0075	0.2433	-0.1344	0.2933	25.325	18.6321	14.0606
2	3.7006	-0.8558	-0.2594	0.8175	-1.6282	4.9539	0.0504	-0.2498	0.3446	0.1041	0.015	-0.0083	-0.3294	-0.095	-0.0653	0.17	-0.0101	0.0369	0.1829	-0.0926	0.17	11.8171	19.2406	7.8143
3	7.6701	-0.9113	0.7673	2.5538	-0.4815	1.512	-0.0209	-0.1096	0.3137	0.0468	0.1014	-0.4038	-0.1316	0.2232	-0.0804	0.1561	-0.0123	0.0006	0.153	-0.0275	0.0962	22.8992	14.6388	4.3653
4	2.383	-1.5873	-0.5044	2.7335	1.7411	1.2881	0.0321	0.0317	-0.1961	0.0994	-0.0238	0.0861	0.1157	0.0009	-0.0083	0.1529	0.0001	-0.027	0.1539	-0.0102	0.2046	18.7835	-0.2689	-1.5636
5	2.4542	-0.1723	1.3064	1.9826	0.2686	5.014	0.1636	-0.1801	-0.1777	0.1286	0.0203	-0.2715	0.0915	0.4167	-0.1839	0.0882	0.018	-0.034	0.1723	0.0021	0.2397	31.501	4.7613	3.1751
6	4.3366	-3.6239	1.4214	6.0429	2.6327	5.698	-0.0312	-0.7518	-0.6695	0.919	0.6992	-0.0858	1.2093	0.4128	-0.6679	0.3208	0.072	-0.1751	0.8619	0.5768	0.7492	29.9985	-4.0884	11.8694
7	3.0404	1.5625	0.8672	0.957	1.0605	2.7461	0.0694	-0.0536	-0.0796	0.0158	0.0369	-0.0526	-0.1247	0.3663	-0.1063	0.1732	-0.061	0.0084	0.1823	-0.0211	0.1407	16.4936	9.8612	6.28
8	2.8407	-0.9432	-0.5867	3.3263	0.7413	1.4867	0.081	-0.144	-0.1859	-0.0077	-0.0593	0	-0.0334	-0.0938	-0.0217	0.1228	-0.0453	0.0115	0.1109	0.037	0.1064	14.964	3.1581	2.452
9	2.9549	-1.9571	-3.5964	1.9071	2.685	5.9096	0.0287	0.2918	-0.3722	-0.0489	-0.034	-0.1006	0.2257	-0.5767	0.0054	0.1726	-0.0266	-0.0018	0.1965	-0.0276	0.3265	24.2632	-1.7267	-0.0249
10	13.0938	-2.0662	-1.3156	3.0268	4.1241	6.0325	0.1362	-0.6263	-0.2824	0.1456	-0.3377	0.1984	0.099	-0.3631	0.2015	0.1586	-0.1002	0.0734	0.3292	0.0006	0.0679	3.9038	9.5479	16.453
11	11.0244	-5.45	1.6944	6.8438	1.6035	5.3986	-0.0464	0.2272	0.8052	-0.3835	0.0733	0.067	-0.4686	0.178	-0.0269	0.2225	0.0145	-0.0518	0.2146	0.0982	0.2523	-3.6089	41.3631	-25.8471
12	3.7718	0.7318	0.196	2.6384	-0.119	1.9348	0.0356	0.0548	0.2814	0.0279	0.0573	0.0648	-0.0515	-0.0909	-0.0928	0.1195	0.0315	0.0122	0.1297	-0.0002	0.1362	2.0584	39.7366	-16.3326
13	4.0619	0.6351	1.9062	3.8998	-2.1806	2.5143	0.1224	-0.3149	-0.1823	0.013	0.0499	0.1141	0.0802	-0.2001	-0.1723	0.1795	0.0207	-0.0168	0.1319	-0.0013	0.1774	2.2263	23.6207	-10.4382
14	2.4825	1.1775	-4.2822	6.1401	-4.0841	8.293	-0.0138	-0.0834	0.0338	0.3959	-0.0467	0.1976	-0.0704	0.0781	0.0605	0.1046	-0.0091	0.0053	0.1526	-0.0251	0.3022	-11.2162	27.0652	-8.9303
15	5.668	0.7992	-1.9687	3.1782	-1.9666	6.7046	-0.3392	0.5227	-0.4123	-0.4356	0.075	0.3558	0.6689	-0.6685	0.2642	0.1667	-0.1032	-0.0297	0.2312	-0.0806	0.2619	-11.6086	19.4954	-20.9986
16	4.7258	-0.0818	0.8707	0.5349	-0.6178	1.309	-0.0447	0.2843	0.1395	-0.1393	-0.0414	0.0463	0.1397	-0.045	0.0861	0.1615	0.0241	-0.0029	0.1754	-0.0332	0.074	2.4041	30.3144	-20.2977
17	3.6576	1.4285	0.2545	4.0604	-0.3041	1.8919	-0.0002	0.1889	-0.0005	-0.0055	0.0278	-0.172	0.0555	0.1432	-0.0276	0.1012	0.0465	0.0174	0.1159	-0.0419	0.0733	7.3194	28.4024	-15.9437
18	0.2458	0.3702	-1.0999	0.6855	-1.8606	5.2469	-0.0213	-0.0301	0.0002	0.0474	-0.2301	-0.1732	-0.0932	0.3816	0.2513	0.232	0.0028	0.0188	0.3585	0.0779	0.4205	-6.8966	17.0001	-1.2723
19	4.6808	1.2481	-2.4856	2.4041	-1.1644	2.3153	0.0602	0.057	-0.1794	-0.1608	0.0161	0.0401	0.1887	0.1378	-0.0764	0.1285	0.0128	-0.0275	0.137	-0.0576	0.1153	3.9675	25.3907	-20.4279
20	21.9052	12.2831	6.9613	36.5928	4.5773	15.7367	-0.5709	1.4147	1.0542	-0.8834	0.3806	-1.2156	-0.4467	0.2824	0.1903	0.0512	0.0654	-0.0121	0.4983	0.0032	0.1822	19.9392	35.8535	-28.535

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	441 - 448
2	X-RAY DIFFRACTION	2	A	449 - 465
3	X-RAY DIFFRACTION	3	A	466 - 494
4	X-RAY DIFFRACTION	4	A	495 - 527
5	X-RAY DIFFRACTION	5	A	528 - 541
6	X-RAY DIFFRACTION	6	A	542 - 558
7	X-RAY DIFFRACTION	7	A	559 - 569
8	X-RAY DIFFRACTION	8	A	570 - 600
9	X-RAY DIFFRACTION	9	A	601 - 612
10	X-RAY DIFFRACTION	10	A	613 - 632
11	X-RAY DIFFRACTION	11	B	441 - 450
12	X-RAY DIFFRACTION	12	B	451 - 494
13	X-RAY DIFFRACTION	13	B	495 - 514
14	X-RAY DIFFRACTION	14	B	522 - 539
15	X-RAY DIFFRACTION	15	B	540 - 555
16	X-RAY DIFFRACTION	16	B	556 - 569
17	X-RAY DIFFRACTION	17	B	570 - 594
18	X-RAY DIFFRACTION	18	B	595 - 603
19	X-RAY DIFFRACTION	19	B	604 - 622
20	X-RAY DIFFRACTION	20	B	623 - 632

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi