PDB-9biv: Crystal Structure of Ubc13 with a New Active Site Loop Conformation

ID or keywords:

Entry

Database: PDB / ID: 9biv

Title

Crystal Structure of Ubc13 with a New Active Site Loop Conformation

Components

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

Keywords

LIGASE / E2 / Conjugating /

Enzyme /

Ubiquitin / Ubc13 / Mms2

Function / homology

Function and homology information

error-free postreplication DNA repair / : / : / 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-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 / FCERI mediated NF-kB activation / Aggrephagy / 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 /

MOLECULAR REPLACEMENT / Resolution: 1.68 Å

Authors

Farraj, R.A. / Edwards, R.A. / Glover, J.N.M.

Funding support

Canada, 1items

Citation

Journal: To Be Published
Title: Crystal Structure of Ubc13 with a New Active Site Loop Conformation
Authors: Farraj, R.A. / Edwards, R.A. / Glover, J.N.M.

History

Deposition	Apr 24, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 8, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9biv.cif.gz	186.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9biv.ent.gz	150.5 KB	Display	PDB format
PDBx/mmJSON format	9biv.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/bi/9biv ftp://data.pdbj.org/pub/pdb/validation_reports/bi/9biv	HTTPS FTP

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Related structure data

Similar structure data	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

33.5 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)	86.361, 42.942, 93.790
Angle α, β, γ (deg.)	90.00, 108.37, 90.00
Int Tables number	5
Space group name H-M	C121

#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: 16380.731 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2V2, MMS2, UEV2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15819
#2: Protein	Ubiquitin-conjugating enzyme E2 N / Bendless-like ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme N / Ubc13 / UbcH13 / ...Bendless-like ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme N / Ubc13 / UbcH13 / Ubiquitin carrier protein N / Ubiquitin-protein ligase N Mass: 17157.770 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2N, BLU / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P61088, E2 ubiquitin-conjugating enzyme
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 442 / 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: 2.46 Å³/Da / Density % sol: 50.01 %
Crystal grow	Temperature: 298 K / Method: batch mode / pH: 7.5 Details: Ubc13-Mms2 heterodimer was concentrated to 12 mg/mL and stored in 50 mM Tris pH 7.5, 150 mM NaCl, 1mM TCEP. Complex was left to slowly equilibrate from 277K to 298 overnight

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
Detector	Type: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Dec 15, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54178 Å / Relative weight: 1
Reflection	Resolution: 1.68→50 Å / Num. obs: 37365 / % possible obs: 99.9 % / Redundancy: 7.6 % / CC_1/2: 0.94 / CC star: 0.984 / Net I/σ(I): 5.37
Reflection shell	Resolution: 1.68→1.71 Å / Num. unique obs: 1843 / CC_1/2: 0.94 / R_rim(I) all: 0.286

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Processing

Software

Name	Version	Classification
PHENIX	(1.16_3546: ???)	refinement
HKL-2000		data scaling
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.68→42.684 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.7 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1766	1920	5.14 %
R_work	0.1438	-	-
obs	0.1454	37360	99.62 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.68→42.684 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2293	0	0	442	2735

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	2346
X-RAY DIFFRACTION	f_angle_d	0.803	3185
X-RAY DIFFRACTION	f_dihedral_angle_d	12.289	1452
X-RAY DIFFRACTION	f_chiral_restr	0.053	347
X-RAY DIFFRACTION	f_plane_restr	0.006	418

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 (%)
1.6805-1.7225	0.1943	131	0.175	2439	X-RAY DIFFRACTION	95
1.7225-1.7691	0.1929	150	0.1686	2472	X-RAY DIFFRACTION	100
1.7691-1.8211	0.2057	133	0.1651	2484	X-RAY DIFFRACTION	100
1.8211-1.8799	0.189	139	0.1555	2541	X-RAY DIFFRACTION	100
1.8799-1.9471	0.1895	138	0.1505	2527	X-RAY DIFFRACTION	100
1.9471-2.025	0.1717	141	0.1417	2519	X-RAY DIFFRACTION	100
2.025-2.1172	0.161	148	0.1324	2512	X-RAY DIFFRACTION	100
2.1172-2.2288	0.1664	121	0.1317	2550	X-RAY DIFFRACTION	100
2.2288-2.3685	0.19	129	0.138	2536	X-RAY DIFFRACTION	100
2.3685-2.5513	0.1692	130	0.1358	2561	X-RAY DIFFRACTION	100
2.5513-2.808	0.1666	133	0.143	2534	X-RAY DIFFRACTION	100
2.808-3.2142	0.1617	122	0.1388	2590	X-RAY DIFFRACTION	100
3.2142-4.0491	0.1812	153	0.1281	2546	X-RAY DIFFRACTION	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	2.6974	0.7338	-2.1055	1.7737	-0.3152	5.5752	0.0535	-0.2992	0.0458	0.2139	-0.154	-0.0277	-0.1857	0.153	0.1307	0.1172	0.0164	-0.0185	0.1181	-0.0428	0.1072	15.5786	21.0861	23.8
2	2.7074	0.1677	-1.2477	0.8097	0.3471	1.8765	0.0082	0.0409	0.0138	0.0986	-0.0451	0.0812	-0.1106	-0.1382	0.0477	0.1151	0.0182	-0.0079	0.0808	-0.0068	0.1025	13.7521	21.1942	13.1214
3	1.5969	-0.839	-0.3247	2.5459	1.0194	2.4202	0.0448	0.148	0.1355	-0.1223	0.0145	-0.254	-0.0926	0.0194	-0.0278	0.0788	-0.0157	0.0036	0.0587	-0.0003	0.0895	21.4502	13.2362	3.7682
4	5.9432	-1.5048	1.6171	4.5165	2.4157	3.3065	-0.1497	-0.5286	-0.3424	0.3728	0.1274	0.3419	0.2291	-0.0914	-0.007	0.1179	0.0044	0.0404	0.1407	0.023	0.1167	11.739	9.7612	22.4625
5	0.6361	0.2704	0.4406	1.9862	-1.0612	7.2016	0.0031	0.1268	-0.1126	0.0304	-0.021	0.2034	-0.2963	-0.3512	-0.0582	0.0734	-0.0056	-0.0038	0.0579	-0.0099	0.1072	15.1761	7.831	3.2216
6	2.0503	-0.9801	0.9261	1.2556	0.2134	5.884	0.0346	-0.089	-0.2103	0.069	-0.064	0.1969	0.3661	-0.0955	-0.002	0.1288	-0.0086	0.0213	0.0759	0.0011	0.1213	17.2157	1.0834	8.7866
7	2.2879	2.1382	-1.1009	6.4777	3.2769	4.6767	0.0828	-0.317	-0.1241	0.3366	0.0192	-0.1115	0.4967	0.377	-0.1039	0.1433	0.0428	-0.0125	0.1987	0.0164	0.1154	20.8599	7.6801	23.2285
8	4.0031	-2.3466	-2.4764	2.8128	1.8397	3.671	-0.0071	-0.1735	0.0495	0.164	0.1139	-0.1384	0.1292	0.1364	-0.1416	0.0899	-0.0074	-0.013	0.0798	-0.0059	0.1064	25.4084	9.9095	11.1872
9	4.2211	-1.1159	0.5159	4.2204	-0.6714	4.4867	0.022	0.0173	0.0178	-0.0607	-0.0133	0.0835	-0.0443	-0.0813	0.0466	0.0993	-0.0107	0.0081	0.0562	-0.0257	0.0826	21.2188	4.9854	-2.3328
10	5.9423	0.5243	-0.0913	2.6852	-0.9831	2.1033	-0.1552	-0.6842	-0.0071	0.6917	0.1385	-0.2389	0.2555	0.228	-0.0599	0.3822	0.0313	-0.0202	0.2546	-0.0053	0.1232	8.2485	23.6939	47.6467
11	5.1909	-2.3983	0.3607	1.7894	-1.3032	1.9377	0.0247	-0.0903	-0.3545	0.1773	0.0631	0.4915	0.1103	-0.2475	0.003	0.1976	0.0067	0.018	0.1977	0.04	0.1214	-0.4803	22.5773	40.4055
12	3.7236	-1.7242	2.0702	2.7482	-1.3327	2.6062	-0.022	-0.1655	0.0329	0.1301	0.0439	0.1351	0.014	-0.1791	-0.052	0.116	0.0048	0.019	0.1365	-0.0031	0.0813	-1.5022	27.4602	32.161
13	1.8708	0.6873	0.43	5.1499	-1.5914	6.0772	0.0086	-0.286	-0.1955	0.068	0.3021	-0.7546	0.0615	0.5732	-0.099	0.1134	0.0381	-0.0556	0.2558	-0.0531	0.2073	17.0853	27.6578	38.4831
14	1.4468	-0.1923	1.6822	1.1687	-0.0819	4.203	-0.0705	-0.048	0.1866	0.174	-0.0244	-0.083	-0.237	0.1293	0.0378	0.1181	-0.0032	-0.011	0.1076	-0.0145	0.1279	5.3712	33.8503	30.515
15	6.3117	1.1532	-3.471	1.9804	-0.9242	1.9555	0.2862	-0.3912	1.0294	0.2775	0.0341	-0.2057	-0.6575	0.6544	-0.1765	0.3361	-0.0727	-0.0353	0.2961	-0.0029	0.4399	3.8407	44.0341	23.2418
16	3.7317	-0.4735	1.1124	4.2707	-0.1423	3.5159	-0.0304	0.1424	0.269	-0.1474	-0.0446	-0.0585	-0.1906	-0.0644	0.0379	0.0987	0.0215	-0.0229	0.1279	0.0072	0.1273	-6.8648	36.5989	18.4045

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 6 through 24 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 25 through 44 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 45 through 68 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 69 through 78 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 79 through 87 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 88 through 107 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 108 through 114 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 115 through 127 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 128 through 145 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 4 through 17 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 18 through 30 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 31 through 57 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 58 through 67 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 68 through 113 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 114 through 123 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 124 through 151 )

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