PDB-4onn: Crystal structure of human Mms2/Ubc13 - BAY 11-7082

ID or keywords:

Entry

Database: PDB / ID: 4onn

Title

Crystal structure of human Mms2/Ubc13 - BAY 11-7082

Components

Ubiquitin-conjugating enzyme E2 N
Ubiquitin-conjugating enzyme E2 variant 2

Keywords

LIGASE / E2 ubiquitin conjugating enzyme / E1 / E3 /

ubiquitin / covalent adduct

Function / homology

Function and homology information

error-free postreplication DNA repair / : / UBC13-UEV1A complex / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / DNA double-strand break processing / positive regulation of protein K63-linked ubiquitination /

postreplication repair / positive regulation of double-strand break repair ...error-free postreplication DNA repair / : / UBC13-UEV1A complex / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / DNA double-strand break processing / positive regulation of protein K63-linked ubiquitination /

postreplication repair / positive regulation of double-strand break repair /

E2 ubiquitin-conjugating enzyme / positive regulation of intracellular signal transduction / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / antiviral innate immune response /

regulation of DNA repair /

ubiquitin ligase complex / negative regulation of TORC1 signaling / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / positive regulation of DNA repair / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 /

ubiquitin binding / activated TAK1 mediates p38 MAPK activation / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / G2/M DNA damage checkpoint / ISG15 antiviral mechanism / CLEC7A (Dectin-1) signaling / Formation of Incision Complex in GG-NER / Aggrephagy / FCERI mediated NF-kB activation / Interleukin-1 signaling / protein polyubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / positive regulation of NF-kappaB transcription factor activity / Processing of DNA double-strand break ends / T cell receptor signaling pathway / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / protein ubiquitination /

ubiquitin protein ligase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein-containing complex /

RNA binding / extracellular exosome /

nucleoplasm /

ATP binding /

nucleus /

cytosol /

cytoplasm
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Hodge, C.D. / Edwards, R.A. / Glover, J.N.M.

Citation

Journal: Acs Chem.Biol. / Year: 2015
Title: Covalent Inhibition of Ubc13 Affects Ubiquitin Signaling and Reveals Active Site Elements Important for Targeting.
Authors: Hodge, C.D. / Edwards, R.A. / Markin, C.J. / McDonald, D. / Pulvino, M. / Huen, M.S. / Zhao, J. / Spyracopoulos, L. / Hendzel, M.J. / Glover, J.N.

History

Deposition	Jan 28, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 6, 2015	Provider: repository / Type: Initial release
Revision 1.1	Aug 5, 2015	Group: Database references
Revision 1.2	Nov 22, 2017	Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4onn.cif.gz	133 KB	Display	PDBx/mmCIF format
PDB format	pdb4onn.ent.gz	110.7 KB	Display	PDB format
PDBx/mmJSON format	4onn.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/on/4onn ftp://data.pdbj.org/pub/pdb/validation_reports/on/4onn	HTTPS FTP

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Related structure data

Related structure data	4onlC 4onmC C: citing same article (ref.)
Similar structure data	4nrg-d 3von-15 4onl-d 4nr3-d 1jat-d 3von-14 1j7d-d 4dgs-d 3von-18 3von-2 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	#60 - Dec 2004 Ubiquitin similarity (14) #234 - Jun 2019 MDM2 and Cancer similarity (13) #55 - Jul 2004 DNA Ligase similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

Deposited unit

A: Ubiquitin-conjugating enzyme E2 variant 2

B: Ubiquitin-conjugating enzyme E2 N

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	44.730, 74.533, 91.531
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Ubiquitin-conjugating enzyme E2 variant 2 / DDVit 1 / Enterocyte differentiation-associated factor 1 / EDAF-1 / Enterocyte differentiation- ...DDVit 1 / Enterocyte differentiation-associated factor 1 / EDAF-1 / Enterocyte differentiation-promoting factor 1 / EDPF-1 / MMS2 homolog / Vitamin D3-inducible protein Mass: 17165.590 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MMS2, UBE2V2, UEV2 / Plasmid: pGEX6p1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15819
#2: Protein	Ubiquitin-conjugating enzyme E2 N / Bendless-like ubiquitin-conjugating enzyme / Ubc13 / UbcH13 / Ubiquitin carrier protein N / ...Bendless-like ubiquitin-conjugating enzyme / Ubc13 / UbcH13 / Ubiquitin carrier protein N / Ubiquitin-protein ligase N Mass: 17942.631 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BLU, UBE2N / Plasmid: pGEX6p1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61088, ubiquitin-protein ligase
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-BY1 / 3-[(4-methylphenyl)sulfonyl]prop-2-enenitrile / BAY 11-7082 Mass: 207.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₉NO₂S
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H₂O
Nonpolymer details	THE COMPOUND BY1 LOSES THE 4-METHYLBENZENE-SULFINIC ACID GROUP ON INERACTING WITH UBC13 AND THE ...THE COMPOUND BY1 LOSES THE 4-METHYLBENZENE-SULFINIC ACID GROUP ON INERACTING WITH UBC13 AND THE REMAINING PART OF BY1 FORMS A COVALENT BOND WITH THE SG ATOM OF CYS B87

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.17 Å³/Da / Density % sol: 43.39 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 100 mM sodium citrate, 15% PEG 8000, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 105 K

Diffraction source

Source:

SYNCHROTRON / Site:

CLSI

/ Beamline: 08B1-1 / Wavelength: 0.97947 Å

Detector

Type: RAYONIX MX300HE / Detector: CCD / Date: Sep 7, 2013 / Details: Mirrors

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97947 Å / Relative weight: 1

Reflection

Resolution: 1.5→100 Å / Num. obs: 47161 / % possible obs: 99.9 % / Redundancy: 3.5 % / B_iso Wilson estimate: 18.67 Å² / R_merge(I) obs: 0.044 / Χ²: 0.831 / Net I/σ(I): 19.8

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.5-1.53	1.9	0.56	4714	1.069	1	99.9
1.53-1.55	1.9	0.448	4758	1.004	1	100
1.55-1.58	1.9	0.391	4712	1.027	1	100
1.58-1.62	1.9	0.326	4726	0.991	1	99.9
1.62-1.65	1.9	0.275	4710	1.017	1	99.9
1.65-1.69	1.9	0.228	4748	1.02	1	99.8
1.69-1.73	1.9	0.194	4759	1.02	1	99.8
1.73-1.78	2.1	0.175	4738	0.978	1	99.9
1.78-1.83	2.3	0.147	4699	0.946	1	99.7
1.83-1.89	2.6	0.118	4722	0.904	1	99.6
1.89-1.96	2.9	0.106	4708	0.97	1	99.6
1.96-2.04	3.3	0.097	4769	1.023	1	99.7
2.04-2.13	3.8	0.101	4722	1.216	1	99.7
2.13-2.24	4.6	0.077	4739	1.037	1	100
2.24-2.38	5.7	0.068	4726	0.919	1	100
2.38-2.56	5.9	0.05	4734	0.788	1	100
2.56-2.82	5.9	0.041	4752	0.589	1	100
2.82-3.23	5.9	0.048	4762	0.849	1	100
3.23-4.07	5.8	0.034	4740	0.486	1	100
4.07-100	5.5	0.032	4743	0.482	1	99.8

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHENIX	1.8.3_1479	refinement
PDB_EXTRACT	3.14	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.5→45.766 Å / FOM work R set: 0.8557 / SU ML: 0.17 / σ(F): 0.04 / Phase error: 21.52 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2132	2635	5.31 %
R_work	0.1791	-	-
obs	0.1809	47161	99.86 %

Solvent computation

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

Displacement parameters

B_iso max: 93.49 Å² / B_iso mean: 28.85 Å² / B_iso min: 11.3 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→45.766 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2295	0	22	183	2500

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2438
X-RAY DIFFRACTION	f_angle_d	1.144	3314
X-RAY DIFFRACTION	f_chiral_restr	0.077	354
X-RAY DIFFRACTION	f_plane_restr	0.005	437
X-RAY DIFFRACTION	f_dihedral_angle_d	13.506	948

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.5-1.5161	0.3335	151	0.303	2866	3017	97
1.5161-1.5339	0.2815	219	0.2828	2977	3196	100
1.5339-1.5526	0.2777	156	0.2625	3023	3179	100
1.5526-1.5723	0.2933	171	0.2534	2955	3126	100
1.5723-1.593	0.2825	160	0.2533	3037	3197	100
1.593-1.6148	0.2748	155	0.2409	2969	3124	100
1.6148-1.6379	0.2583	167	0.2367	3016	3183	100
1.6379-1.6623	0.2361	156	0.2281	2996	3152	100
1.6623-1.6883	0.2659	173	0.2174	2977	3150	100
1.6883-1.716	0.2137	189	0.2088	2974	3163	100
1.716-1.7456	0.2475	157	0.2175	2992	3149	100
1.7456-1.7773	0.2629	191	0.199	3006	3197	100
1.7773-1.8115	0.2094	194	0.1955	2929	3123	100
1.8115-1.8485	0.2418	170	0.1907	3012	3182	100
1.8485-1.8887	0.2447	156	0.1788	2988	3144	100
1.8887-1.9326	0.2434	138	0.1798	3036	3174	100
1.9326-1.9809	0.208	167	0.1836	2977	3144	100
1.9809-2.0345	0.2326	181	0.1781	3010	3191	100
2.0345-2.0943	0.2114	137	0.1711	2958	3095	100
2.0943-2.1619	0.2237	149	0.1752	3043	3192	100
2.1619-2.2392	0.2017	209	0.1772	2974	3183	100
2.2392-2.3289	0.1996	178	0.173	2978	3156	100
2.3289-2.4349	0.2253	165	0.1775	2965	3130	100
2.4349-2.5632	0.2316	177	0.1705	3005	3182	100
2.5632-2.7238	0.231	183	0.1823	2960	3143	100
2.7238-2.9341	0.2351	148	0.1818	3019	3167	100
2.9341-3.2293	0.2514	183	0.1779	3007	3190	100
3.2293-3.6964	0.169	146	0.164	3000	3146	100
3.6964-4.6563	0.175	147	0.1491	3018	3165	100
4.6563-45.766	0.1596	156	0.1602	2998	3154	100

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	1.9636	-0.741	0.2614	1.8835	1.5149	9.2692	-0.1077	-0.024	-0.1689	0.3219	-0.0821	-0.0748	0.6161	0.1375	0.1753	0.1692	-0.0167	-0.0177	0.1731	0.0086	0.1787	22.0957	14.2108	18.7585
2	4.566	0.318	3.0055	1.6026	0.6789	5.6938	-0.2119	0.3406	0.09	-0.089	0.1304	-0.1428	-0.3167	0.5367	0.0363	0.0922	-0.0245	0.0185	0.1251	0.0274	0.1187	17.6325	19.5016	7.2721
3	1.7156	0.1627	1.3917	1.8541	-0.221	8.5319	-0.1455	-0.0374	0.1605	0.1954	0.0446	0.0396	-0.403	0.1213	0.1115	0.103	0.0136	-0.0032	0.0895	-0.0127	0.1248	11.6131	21.6241	12.5574
4	1.2951	0.464	1.443	5.4004	-3.5984	6.9527	-0.1578	0.0032	0.2266	0.267	0.1906	0.4614	-0.3879	-0.502	-0.0853	0.1276	0.0343	0.0138	0.2055	0.0003	0.2064	2.5337	20.0811	9.5817
5	2.4475	0.2004	1.6149	2.5521	-0.2011	5.5871	0.0848	0.0372	-0.2157	0.2322	0.0218	0.1129	0.1895	0.041	-0.11	0.13	0.0013	0.012	0.0926	-0.0099	0.1662	10.1034	10.6987	13.7377
6	8.4443	2.6279	-0.5409	1.4364	-1.6938	6.4688	-0.1638	0.1891	0.2494	-0.1648	0.1021	0.1208	-0.2216	0.1488	0.0135	0.1234	0.0248	-0.026	0.1907	-0.0283	0.1396	5.8539	19.5265	-1.9516
7	8.5591	0.4151	-1.4984	6.8213	1.4921	6.684	0.2388	-0.5236	0.2292	0.0293	-0.3237	-0.7467	-0.3631	0.8081	0.0692	0.3953	-0.0346	0.0282	0.3969	0.1389	0.4063	25.4435	11.2278	47.6725
8	4.1529	3.3262	1.3318	2.712	1.199	0.9897	0.3223	-0.6508	0.0176	0.7879	-0.3053	0.1642	-0.058	-0.2733	-0.0376	0.4696	-0.112	0.0028	0.3553	0.0795	0.2787	24.8374	21.9671	44.0742
9	5.2496	4.4474	-0.3351	7.1064	0.6015	1.7811	0.2808	-0.1375	0.0081	0.5566	-0.0798	-0.0674	0.1076	-0.0082	-0.2078	0.2173	0.0065	-0.0539	0.1476	0.0355	0.1388	32.1268	28.5369	36.9899
10	2.9909	1.6424	-1.6222	7.2928	-3.105	3.2339	-0.3587	-0.0745	-0.5082	-0.403	0.2823	0.1746	0.6211	-0.2034	0.0473	0.2516	-0.0095	0.0112	0.1563	0.0224	0.2341	29.6536	17.3429	32.524
11	2.0145	0.9497	1.2859	5.2384	-0.231	4.3452	0.0629	0.4192	-0.2442	-0.0998	0.0951	-0.3674	0.3633	0.016	-0.1131	0.1577	0.0249	-0.0178	0.1579	-0.0388	0.1943	35.5862	24.6987	24.9342
12	2.1712	2.6155	-3.0618	5.1041	-6.7374	9.0015	-0.2729	-0.5288	-1.0202	-0.3107	-0.3546	-0.8405	0.9861	0.918	0.6747	0.4912	0.0797	0.0941	0.5358	0.2614	0.6578	38.2233	11.5359	34.4827
13	5.0573	4.7637	-5.1519	7.081	-6.4315	8.1115	-0.0535	-1.2174	-0.9418	0.4853	-0.3866	-0.6089	-0.0855	0.2751	0.3946	0.2354	0.0299	-0.0375	0.3379	0.1228	0.2923	37.9148	21.5968	39.7582
14	1.5324	0.8664	0.3984	3.5431	4.8316	7.0944	0.0336	0.2195	-0.3937	0.0106	-0.0239	-0.3672	0.3185	-0.2773	0.03	0.2591	0.0294	0.0189	0.3116	-0.076	0.4314	46.1736	22.9393	24.5733
15	3.4812	3.9177	3.9377	7.3166	1.6314	7.167	0.5921	1.3176	0.1698	-1.3922	-0.1681	-0.69	-0.4042	0.5119	-0.3896	0.3949	0.1065	0.1868	0.3552	-0.0152	0.5772	46.7226	31.3172	21.0783
16	2.0011	-1.1681	-0.854	8.228	0.2429	6.7003	0.1397	-0.347	0.1103	-0.0104	0.0919	-0.3788	-0.2027	0.1147	-0.2231	0.1848	0.0123	-0.0052	0.1147	0.0003	0.1633	37.9814	38.8858	28.3274

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 6 through 35 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 36 through 61 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 62 through 87 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 88 through 107 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 108 through 127 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 128 through 145 )	A
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 2 through 15 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 16 through 33 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 34 through 57 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 58 through 76 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 77 through 86 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 87 through 100 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 101 through 113 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 114 through 123 )	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 124 through 132 )	B
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 133 through 150 )	B

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