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- PDB-4onl: Crystal structure of human Mms2/Ubc13_D81N, R85S, A122V, N123P -

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Basic information

Entry
Database: PDB / ID: 4onl
TitleCrystal structure of human Mms2/Ubc13_D81N, R85S, A122V, N123P
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-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
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsHodge, C.D. / Edwards, R.A. / Glover, J.N.M.
CitationJournal: 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
DepositionJan 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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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)35,0482
Polymers35,0482
Non-polymers00
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-10 kcal/mol
Surface area15310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.933, 74.942, 92.055
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 / Mutation: R85S, A122V, N123P
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: 17882.596 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.16 Å3/Da / Density % sol: 43.11 %
Crystal growTemperature: 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

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.03316 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 13, 2013 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03316 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 66851 / % possible obs: 98.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 15.26 Å2 / Rmerge(I) obs: 0.034 / Χ2: 1.001 / Net I/σ(I): 19.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.35-1.373.50.60732730.957197.2
1.37-1.43.50.52332880.917199.6
1.4-1.433.50.44832710.985198.6
1.43-1.453.50.35833311.046199.5
1.45-1.493.60.29432871.032199.2
1.49-1.523.60.25333491.053199.4
1.52-1.563.60.20933231.051199.8
1.56-1.63.70.16733231.049199.6
1.6-1.653.70.13633271.011199.7
1.65-1.73.80.11633561.049199.7
1.7-1.763.80.09333421.049199.8
1.76-1.833.80.07333651.011199.8
1.83-1.923.80.05333610.96199.8
1.92-2.023.90.04633470.969199.8
2.02-2.143.80.04233791.1199.7
2.14-2.313.80.04433870.927199.8
2.31-2.543.80.03833850.959199.9
2.54-2.913.60.02734131.072198.9
2.91-3.663.80.0234090.829198.5
3.66-503.90.01833351.007191.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.3_1479refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→29.059 Å / FOM work R set: 0.8875 / SU ML: 0.13 / σ(F): 1.36 / Phase error: 18.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1994 3555 5.32 %
Rwork0.1711 --
obs0.1727 66798 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.96 Å2 / Biso mean: 24.14 Å2 / Biso min: 8.57 Å2
Refinement stepCycle: LAST / Resolution: 1.35→29.059 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2291 0 0 197 2488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112418
X-RAY DIFFRACTIONf_angle_d1.3963301
X-RAY DIFFRACTIONf_chiral_restr0.095359
X-RAY DIFFRACTIONf_plane_restr0.009434
X-RAY DIFFRACTIONf_dihedral_angle_d13.774955
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.35-1.36840.27371320.21542398253095
1.3684-1.38790.24041400.22485262598
1.3879-1.40860.26081400.18992507264799
1.4086-1.43070.21161420.17532477261999
1.4307-1.45410.23731500.160225292679100
1.4541-1.47920.17561340.15012516265099
1.4792-1.50610.20961450.138325112656100
1.5061-1.5350.15551330.13872510264399
1.535-1.56640.18141320.132425562688100
1.5664-1.60040.18331410.130825002641100
1.6004-1.63770.19231540.132825212675100
1.6377-1.67860.17781560.129625312687100
1.6786-1.7240.17321570.135925122669100
1.724-1.77470.1751420.135125422684100
1.7747-1.8320.19741390.142725552694100
1.832-1.89750.19731500.145525212671100
1.8975-1.97340.20371280.149825702698100
1.9734-2.06320.17441450.150125292674100
2.0632-2.17190.19241240.162725982722100
2.1719-2.3080.20911680.170425412709100
2.308-2.48610.20481410.173525832724100
2.4861-2.73610.22111570.19112549270699
2.7361-3.13160.21451470.19812573272099
3.1316-3.94390.19791350.1862616275199
3.9439-29.0590.18921230.18982513263690

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