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- PDB-1j7d: Crystal Structure of hMms2-hUbc13 -

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Basic information

Entry
Database: PDB / ID: 1j7d
TitleCrystal Structure of hMms2-hUbc13
Components
  • MMS2
  • UBIQUITIN-CONJUGATING ENZYME E2-17 KDA
KeywordsUNKNOWN FUNCTION / Ubiquitin / Ubc / DNA repair / Traf6 / NFkB
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 / 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 / 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 / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsMoraes, T.F. / Edwards, R.A. / McKenna, S. / Pashushok, L. / Xiao, W. / Glover, J.N.M. / Ellison, M.J.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Crystal structure of the human ubiquitin conjugating enzyme complex, hMms2-hUbc13.
Authors: Moraes, T.F. / Edwards, R.A. / McKenna, S. / Pastushok, L. / Xiao, W. / Glover, J.N. / Ellison, M.J.
History
DepositionMay 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MMS2
B: UBIQUITIN-CONJUGATING ENZYME E2-17 KDA


Theoretical massNumber of molelcules
Total (without water)33,5392
Polymers33,5392
Non-polymers00
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-9 kcal/mol
Surface area14990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.132, 74.137, 91.489
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MMS2


Mass: 16380.731 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q15819
#2: Protein UBIQUITIN-CONJUGATING ENZYME E2-17 KDA / Ubc13


Mass: 17157.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P61088, ubiquitin-protein ligase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.23 Å3/Da / Density % sol: 44.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 8000, 100mM Citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20-24 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
250 mMHEPES1drop
375 mM1dropNaCl
41 mMEDTA1drop
50.5 mMdithiothreitol1drop
620 %(w/v)PEG80001reservoir
7100 mMcitrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.981958, 0.982127, 1.022130
DetectorType: BRANDEIS - B1 / Detector: CCD / Date: Oct 10, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9819581
20.9821271
31.022131
ReflectionResolution: 1.85→40 Å / Num. all: 26066 / Num. obs: 26066 / % possible obs: 98.3 % / Redundancy: 4.25 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.034 / Rsym value: 0.034 / Net I/σ(I): 37.1
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1161 / Rsym value: 0.263 / % possible all: 89.5
Reflection
*PLUS
Lowest resolution: 40 Å / Num. measured all: 110669 / Rmerge(I) obs: 0.024

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 1.85→40 Å / Stereochemistry target values: CNS targets
RfactorNum. reflection% reflectionSelection details
Rfree0.2443 1317 -RANDOM
Rwork0.2149 ---
all-26340 --
obs-25927 98.4 %-
Refinement stepCycle: LAST / Resolution: 1.85→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2295 0 0 190 2485
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.54
X-RAY DIFFRACTIONc_bond_d0.006
LS refinement shellResolution: 1.85→1.87 Å
RfactorNum. reflection% reflection
Rfree0.3147 46 -
Rwork0.2811 --
obs-837 84.6 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 40 Å / % reflection Rfree: 5 % / Rfactor obs: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS

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