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- PDB-2f4w: Human ubiquitin-conjugating enzyme E2 J2 -

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Basic information

Entry
Database: PDB / ID: 2f4w
TitleHuman ubiquitin-conjugating enzyme E2 J2
Componentsubiquitin-conjugating enzyme E2, J2
KeywordsLIGASE / Endoplasmic reticulum / Ubl conjugation pathway / Structural Genomics Consortium (SGC)
Function / homology
Function and homology information


protein K6-linked ubiquitination / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / ubiquitin conjugating enzyme activity / ubiquitin ligase complex / response to unfolded protein / ERAD pathway / protein polyubiquitination / Antigen processing: Ubiquitination & Proteasome degradation ...protein K6-linked ubiquitination / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / ubiquitin conjugating enzyme activity / ubiquitin ligase complex / response to unfolded protein / ERAD pathway / protein polyubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / ubiquitin-dependent protein catabolic process / ubiquitin protein ligase binding / endoplasmic reticulum membrane / endoplasmic reticulum / ATP binding / nucleus / 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 J2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWalker, J.R. / Avvakumov, G.V. / Xue, S. / Finerty Jr., P.J. / Newman, E.M. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. ...Walker, J.R. / Avvakumov, G.V. / Xue, S. / Finerty Jr., P.J. / Newman, E.M. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
Citation
Journal: 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.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: Endoplasmic reticulum (ER)-associated degradation of T cell receptor subunits. Involvement of ER-associated ubiquitin-conjugating enzymes (E2s).
Authors: Tiwari, S. / Weissman, A.M.
History
DepositionNov 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 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, J2
B: ubiquitin-conjugating enzyme E2, J2


Theoretical massNumber of molelcules
Total (without water)42,6652
Polymers42,6652
Non-polymers00
Water4,414245
1
A: ubiquitin-conjugating enzyme E2, J2


Theoretical massNumber of molelcules
Total (without water)21,3331
Polymers21,3331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ubiquitin-conjugating enzyme E2, J2


Theoretical massNumber of molelcules
Total (without water)21,3331
Polymers21,3331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.070, 48.014, 91.032
Angle α, β, γ (deg.)90.00, 93.94, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-301-

HOH

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Components

#1: Protein ubiquitin-conjugating enzyme E2, J2


Mass: 21332.525 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2J2 / Plasmid: pET-28LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: GenBank: 56206319, UniProt: Q8N2K1*PLUS, ubiquitin-protein ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 35.75 %
Crystal growTemperature: 298 K / Details: VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.00769
DetectorType: SBC-3 / Detector: CCD / Date: Nov 4, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00769 Å / Relative weight: 1
ReflectionResolution: 2→30.84 Å / Num. obs: 23045 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 23.67
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 4.74 / % possible all: 85.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AYZ

1ayz


Resolution: 2→30.84 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.731 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25015 1148 5.1 %RANDOM
Rwork0.18619 ---
obs0.18962 21287 96.5 %-
all-23000 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.137 Å2
Baniso -1Baniso -2Baniso -3
1--2.41 Å20 Å21.33 Å2
2---3.06 Å20 Å2
3---5.65 Å2
Refinement stepCycle: LAST / Resolution: 2→30.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2434 0 0 245 2679
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222506
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6421.9793402
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4715295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.38423.396106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.64715433
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6261514
X-RAY DIFFRACTIONr_chiral_restr0.1030.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021884
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.21157
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.21713
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2194
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2780.276
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2530.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.56431559
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.56742463
X-RAY DIFFRACTIONr_scbond_it4.50251112
X-RAY DIFFRACTIONr_scangle_it6.0337939
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 74 -
Rwork0.249 1478 -
obs--93.55 %

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