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- PDB-4nrg: Crystal Structure of a human Mms2/Ubc13 D118G mutant -

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Basic information

Entry
Database: PDB / ID: 4nrg
TitleCrystal Structure of a human Mms2/Ubc13 D118G mutant
Components
  • Ubiquitin-conjugating enzyme E2 N
  • Ubiquitin-conjugating enzyme E2 variant 2
KeywordsLIGASE / ubc13 / mms2 / E2 / ubiquitin conjugating enzyme
Function / homology
Function and homology information


error-free postreplication DNA repair / : / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / postreplication repair / positive regulation of double-strand break repair / positive regulation of intracellular signal transduction ...error-free postreplication DNA repair / : / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / postreplication repair / positive regulation of double-strand break repair / positive regulation of intracellular signal transduction / E2 ubiquitin-conjugating enzyme / protein K63-linked ubiquitination / ubiquitin conjugating enzyme activity / 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 / T cell receptor signaling pathway / Processing of DNA double-strand break ends / 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
Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 N / Ubiquitin-conjugating enzyme E2 variant 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHodge, C.D. / Edwards, R.A. / Glover, J.N.M.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: Stochastic gate dynamics regulate the catalytic activity of ubiquitination enzymes.
Authors: Rout, M.K. / Hodge, C.D. / Markin, C.J. / Xu, X. / Glover, J.N. / Xiao, W. / Spyracopoulos, L.
History
DepositionNov 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 variant 2
B: Ubiquitin-conjugating enzyme E2 N


Theoretical massNumber of molelcules
Total (without water)35,0502
Polymers35,0502
Non-polymers00
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-9 kcal/mol
Surface area15320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.272, 73.616, 92.093
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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: pHis-P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIPL / 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: 17884.594 Da / Num. of mol.: 1 / Mutation: D118G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BLU, UBE2N / Plasmid: pHis-P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIPL / References: UniProt: P61088, ubiquitin-protein ligase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 20% PEG 8000, 0.1 M sodium citrate, pH 6.8, vapor diffusion, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 4, 2013 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 21609 / Num. obs: 21609 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 26.98 Å2 / Rmerge(I) obs: 0.09 / Χ2: 0.996 / Net I/σ(I): 15.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-1.983.80.4399700.797189.3
1.98-2.0240.37810500.919192.8
2.02-2.064.10.34210161.004191.9
2.06-2.14.10.30310561.083193.5
2.1-2.154.20.26310301.046193.8
2.15-2.24.20.23210561.024194.4
2.2-2.254.20.2210521.04194.2
2.25-2.314.30.19210561.027194.4
2.31-2.384.30.16710611.011194.7
2.38-2.464.30.15210791.014195.6
2.46-2.544.30.13710571.011195.7
2.54-2.654.30.13710690.984196
2.65-2.774.30.12811121.027196.6
2.77-2.914.30.11410850.985196.4
2.91-3.14.30.10111000.978196.8
3.1-3.334.20.0911060.989197.5
3.33-3.674.20.08111270.938197.5
3.67-4.24.10.07311391.041198.5
4.2-5.294.10.06211580.94198.5
5.29-503.90.04112301.022197.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1J7D

1j7d


Resolution: 1.95→22.136 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8427 / SU ML: 0.2 / σ(F): 1.37 / Phase error: 22.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2108 1126 5.22 %random
Rwork0.1782 ---
obs0.1799 21572 95.2 %-
all-21572 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.81 Å2 / Biso mean: 36.1097 Å2 / Biso min: 9.88 Å2
Refinement stepCycle: LAST / Resolution: 1.95→22.136 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2278 0 0 165 2443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052394
X-RAY DIFFRACTIONf_angle_d0.863256
X-RAY DIFFRACTIONf_chiral_restr0.059350
X-RAY DIFFRACTIONf_plane_restr0.003432
X-RAY DIFFRACTIONf_dihedral_angle_d11.801936
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9485-2.03710.29051280.23742357248589
2.0371-2.14450.27471180.20992479259793
2.1445-2.27870.23111650.192458262394
2.2787-2.45440.24531350.18582552268795
2.4544-2.7010.22671530.19852517267096
2.701-3.0910.23951490.19382600274997
3.091-3.89080.19171380.16942655279398
3.8908-22.13740.17081400.15422828296899
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
13.4792-0.96440.49722.4591.69077.7705-0.0699-0.037-0.17230.3387-0.1105-0.15060.53030.05740.21490.13-0.0136-0.02430.14970.00240.186421.834413.980318.9881
23.04230.05541.89751.37190.1395.0151-0.23060.0040.08020.13740.0087-0.0339-0.18110.13670.16770.11510.01720.00250.1194-0.0450.184815.76519.996311.1504
33.63540.7021.78542.6702-1.24234.7275-0.0706-0.28480.01420.13390.12710.13950.0264-0.3642-0.06380.09660.02280.02080.1504-0.04160.13546.981116.327310.3556
47.60250.2343-1.07647.4418-1.19388.2037-0.35550.28420.3-0.17450.26930.2644-0.14860.25420.08430.11190.0237-0.04970.1836-0.07720.15555.874219.3085-1.996
55.06162.16210.43898.30175.27099.64060.3577-0.08710.56950.227-0.3037-0.37930.1890.7698-0.01930.50950.08210.03520.4180.08780.489825.221812.022348.1338
64.34332.32634.3555.14583.01634.8413-0.8436-1.0462-0.17040.51910.51090.14450.0252-1.41380.21650.6202-0.1044-0.0290.52110.09180.283829.236125.009746.342
79.39557.125-1.7919.5831-0.05862.47270.37280.00410.27980.8183-0.03290.22670.13930.0119-0.30520.31930.0571-0.05480.15680.01570.11828.844426.001137.6355
84.6380.92080.20336.7551-2.24692.8061-0.12540.0841-0.6279-0.0080.19070.25770.71550.2116-0.09830.35660.06310.00670.1928-0.06280.191529.366217.512132.5592
92.80110.08771.62685.1512-2.73122.6077-0.078-0.0969-0.8935-0.3720.0812-0.15910.98340.44640.06670.43130.21850.0440.38420.01710.395137.098716.656230.8206
104.78213.9543-4.22393.5936-3.56993.84540.0415-1.5902-1.01670.7972-0.1694-0.7342-0.54540.18640.1510.38160.085-0.09560.48610.11810.310537.753121.431940.2244
117.74891.68713.721.95941.36065.4871-0.17861.8645-1.4361-0.83391.1475-0.63660.4346-0.6829-0.7680.4816-0.09130.12511.1196-0.25410.648246.257527.401322.9479
124.9447-3.58081.69366.7982-0.62494.6541-0.11570.52390.48870.15890.1767-0.384-0.66580.7433-0.12920.17-0.05420.01580.3262-0.00850.172138.273338.536928.3558
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 35 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 78 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 79 through 127 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 128 through 145 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 17 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 18 through 27 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 28 through 57 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 58 through 76 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 77 through 100 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 101 through 113 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 114 through 132 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 133 through 150 )B0

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