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- PDB-2awf: Structure of human Ubiquitin-conjugating enzyme E2 G1 -

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Basic information

Entry
Database: PDB / ID: 2awf
TitleStructure of human Ubiquitin-conjugating enzyme E2 G1
ComponentsUbiquitin-conjugating enzyme E2 G1
KeywordsLIGASE / Ubl conjugation pathway / ubiquitin-conjugating enzyme / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / protein K48-linked ubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / protein polyubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process ...E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / protein K48-linked ubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / protein polyubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitin protein ligase binding / extracellular exosome / ATP binding / cytosol
Similarity search - Function
: / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / 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 ...: / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / 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 G1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWalker, J.R. / Avvakumov, G.V. / Xue, S. / Newman, E.M. / Finerty, P. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. ...Walker, J.R. / Avvakumov, G.V. / Xue, S. / Newman, E.M. / Finerty, P. / 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
DepositionSep 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 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 G1


Theoretical massNumber of molelcules
Total (without water)19,6291
Polymers19,6291
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.444, 59.444, 186.812
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 G1 / Ubiquitin-protein ligase G1 / Ubiquitin carrier protein G1 / E217K / UBC7


Mass: 19629.270 Da / Num. of mol.: 1 / Fragment: catalytic (UBCc) domain, residues 7-159
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2G1, UBE2G / Plasmid: PET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62253, ubiquitin-protein ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 3.48 Å3/Da / Density % sol: 64.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 24% PEG3350, 0.2 M MgAc, 0.1 M Tris, pH 7.5, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97985 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 23, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97985 Å / Relative weight: 1
ReflectionResolution: 2.01→39.7 Å / Num. all: 13412 / Num. obs: 13412 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 15.5 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 72.07
Reflection shellResolution: 2.01→2.08 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.647 / Mean I/σ(I) obs: 2.25 / Num. unique all: 1123 / % possible all: 84.6

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Processing

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

1pzv


Resolution: 2.1→36.98 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.166 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26337 595 5 %RANDOM
Rwork0.22091 ---
all0.257 ---
obs0.22289 11341 97.95 %-
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: 49.808 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20.48 Å20 Å2
2--0.96 Å20 Å2
3----1.44 Å2
Refinement stepCycle: LAST / Resolution: 2.1→36.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms978 0 0 53 1031
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221006
X-RAY DIFFRACTIONr_angle_refined_deg1.571.9851371
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6345120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.94623.95343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.47315169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.492156
X-RAY DIFFRACTIONr_chiral_restr0.1080.2153
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02756
X-RAY DIFFRACTIONr_nbd_refined0.2140.2385
X-RAY DIFFRACTIONr_nbtor_refined0.3190.2668
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.253
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2650.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.23
X-RAY DIFFRACTIONr_mcbond_it2.6053635
X-RAY DIFFRACTIONr_mcangle_it4.03941004
X-RAY DIFFRACTIONr_scbond_it4.6635429
X-RAY DIFFRACTIONr_scangle_it7.387367
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 45 -
Rwork0.289 739 -
obs--89.6 %

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