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- PDB-2a4d: Structure of the human ubiquitin-conjugating enzyme E2 variant 1 ... -

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Basic information

Entry
Database: PDB / ID: 2a4d
TitleStructure of the human ubiquitin-conjugating enzyme E2 variant 1 (UEV-1)
ComponentsUbiquitin-conjugating enzyme E2 variant 1
KeywordsLIGASE / Alternative splicing / Nuclear protein / Ubl conjugation pathway / UBIQUITIN / UBIQUITIN- CONJUGATING ENZYME / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


error-free postreplication DNA repair / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / positive regulation of protein K63-linked ubiquitination / ubiquitin conjugating enzyme binding / DNA damage tolerance / ubiquitin conjugating enzyme activity / positive regulation of intracellular signal transduction / protein K63-linked ubiquitination / ubiquitin ligase complex ...error-free postreplication DNA repair / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / positive regulation of protein K63-linked ubiquitination / ubiquitin conjugating enzyme binding / DNA damage tolerance / ubiquitin conjugating enzyme activity / positive regulation of intracellular signal transduction / protein K63-linked ubiquitination / ubiquitin ligase complex / regulation of DNA repair / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TICAM1, RIP1-mediated IKK complex recruitment / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / TAK1-dependent IKK and NF-kappa-B activation / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / Interleukin-1 signaling / protein polyubiquitination / Aggrephagy / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / cell differentiation / positive regulation of canonical NF-kappaB signal transduction / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein-containing complex / extracellular exosome / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 variant 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsWalker, J.R. / Avvakumov, G.V. / Xue, S. / Newman, E.M. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. ...Walker, J.R. / Avvakumov, G.V. / Xue, S. / Newman, E.M. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: Mol Cell Proteomics / Year: 2012
Title: A human ubiquitin conjugating enzyme (E2)-HECT E3 ligase structure-function screen.
Authors: Sheng, Y. / Hong, J.H. / Doherty, R. / Srikumar, T. / Shloush, J. / Avvakumov, G.V. / Walker, J.R. / Xue, S. / Neculai, D. / Wan, J.W. / Kim, S.K. / Arrowsmith, C.H. / Raught, B. / Dhe-Paganon, S.
History
DepositionJun 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 28, 2012Group: Database references
Revision 1.4Aug 23, 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 1


Theoretical massNumber of molelcules
Total (without water)18,0281
Polymers18,0281
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.058, 53.910, 108.034
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-231-

HOH

DetailsThe biological unit is a monomer.

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 variant 1 / UEV-1 / CROC-1 / Ubiquitin-conjugating enzyme variant Kua / TRAF6-regulated IKK activator 1 beta ...UEV-1 / CROC-1 / Ubiquitin-conjugating enzyme variant Kua / TRAF6-regulated IKK activator 1 beta Uev1A / P/OKcl.19


Mass: 18027.576 Da / Num. of mol.: 1 / Fragment: catalytic domain, residues 82-220
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2V1, CROC1, UBE2V, UEV1 / Plasmid: PET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q13404, ubiquitin-protein ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 1.91 Å3/Da / Density % sol: 35.06 %
Crystal growTemperature: 298 K / pH: 6.5
Details: 32% PEG1500, 0.2 M NaCl, 1 mM DTT, 0.1 M Na cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.54178
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 8, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.69→30 Å / Num. obs: 13994 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 44
Reflection shellResolution: 1.69→1.75 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 2.7 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J7D

1j7d


Resolution: 1.69→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.764 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24 704 5 %RANDOM
Rwork0.183 ---
obs0.185 13262 96.8 %-
all-13966 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2--0.23 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.69→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1104 0 0 69 1173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221128
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.9831526
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.475138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.06824.250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95615206
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.991159
X-RAY DIFFRACTIONr_chiral_restr0.1030.2164
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02852
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.2531
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.2770
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.264
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8693712
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.80641129
X-RAY DIFFRACTIONr_scbond_it5.1015479
X-RAY DIFFRACTIONr_scangle_it6.0737397
X-RAY DIFFRACTIONr_rigid_bond_restr3.7431191
X-RAY DIFFRACTIONr_sphericity_free6.923369
X-RAY DIFFRACTIONr_sphericity_bonded4.92431104
LS refinement shellResolution: 1.69→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 43 -
Rwork0.283 756 -
obs--75.66 %

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