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- PDB-1u9b: MURINE/HUMAN UBIQUITIN-CONJUGATING ENZYME UBC9 -

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Basic information

Entry
Database: PDB / ID: 1u9b
TitleMURINE/HUMAN UBIQUITIN-CONJUGATING ENZYME UBC9
ComponentsUBIQUITIN-CONJUGATING ENZYME E9
KeywordsLIGASE / UBIQUITIN-CONJUGATING ENZYME / UBIQUITIN-DIRECTED PROTEOLYSIS / CELL CYCLE CONTROL
Function / homology
Function and homology information


SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMOylation of nuclear envelope proteins / Vitamin D (calciferol) metabolism / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of ubiquitinylation proteins / SUMOylation of SUMOylation proteins / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / SUMOylation of RNA binding proteins ...SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMOylation of nuclear envelope proteins / Vitamin D (calciferol) metabolism / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of ubiquitinylation proteins / SUMOylation of SUMOylation proteins / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / SUMOylation of RNA binding proteins / SUMOylation of DNA methylation proteins / SUMOylation of DNA damage response and repair proteins / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / SUMOylation of intracellular receptors / SUMOylation of immune response proteins / HLH domain binding / SUMO conjugating enzyme activity / Formation of Incision Complex in GG-NER / RING-like zinc finger domain binding / Processing of DNA double-strand break ends / SUMO ligase complex / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / bHLH transcription factor binding / transferase complex / small protein activating enzyme binding / Transferases; Acyltransferases; Aminoacyltransferases / nuclear export / SUMO transferase activity / protein sumoylation / nuclear pore / ionotropic glutamate receptor binding / chromosome segregation / transcription coregulator binding / protein modification process / fibrillar center / PML body / ubiquitin-protein transferase activity / nuclear envelope / positive regulation of canonical NF-kappaB signal transduction / nuclear body / positive regulation of cell migration / cell division / negative regulation of DNA-templated transcription / dendrite / enzyme binding / negative regulation of transcription by RNA polymerase II / 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
SUMO-conjugating enzyme UBC9
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTong, H. / Hateboer, G. / Perrakis, A. / Bernards, R. / Sixma, T.K.
CitationJournal: J.Biol.Chem. / Year: 1997
Title: Crystal structure of murine/human Ubc9 provides insight into the variability of the ubiquitin-conjugating system.
Authors: Tong, H. / Hateboer, G. / Perrakis, A. / Bernards, R. / Sixma, T.K.
History
DepositionMay 20, 1997Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UBIQUITIN-CONJUGATING ENZYME E9


Theoretical massNumber of molelcules
Total (without water)18,2581
Polymers18,2581
Non-polymers00
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.390, 93.950, 115.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein UBIQUITIN-CONJUGATING ENZYME E9 / UBC9


Mass: 18258.076 Da / Num. of mol.: 1 / Mutation: INS(ASN 0)
Source method: isolated from a genetically manipulated source
Details: MAMMALIAN / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA / References: UniProt: P63280, ubiquitin-protein ligase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.64 Å3/Da / Density % sol: 52 %
Crystal growpH: 6.5
Details: 23% PEG MONOMETHYL ETHER 5000,9% ISOPROPANOL, 0.1 M AMMONIUM SULFATE, 0.1 M MES BUFFER, PH6.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15.5 mg/mlprotein1drop
275 mM1dropNaCl
30.25 mMdithiothreitol1drop
45 mMHEPES1drop
511.5 %PEG50001drop
64.5 %isopropanol1drop
70.05 Mammonium sulfate1drop
80.05 MMES1drop
923 %PEG50001reservoir
109 %isopropanol1reservoir
110.1 Mammonium sulfate1reservoir
120.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 281 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.885
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 26, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.885 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 12854 / % possible obs: 98 % / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Biso Wilson estimate: 29.7 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 17
Reflection shellResolution: 2.02→2.05 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3 / Rsym value: 0.41 / % possible all: 99
Reflection shell
*PLUS
% possible obs: 99 %

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Processing

Software
NameVersionClassification
AMoREphasing
TNT5Drefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AAK

1aak
PDB Unreleased entry


Resolution: 2→10 Å / Isotropic thermal model: TNT BCORREL V1.0 / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflectionSelection details
Rfree0.25 629 5 %RANDOM
Rwork0.185 ---
all-12854 --
obs-12854 98 %-
Solvent computationSolvent model: BABINET SCALING / Bsol: 228.3 Å2 / ksol: 0.8 e/Å3
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1276 0 0 96 1372
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01513130.5
X-RAY DIFFRACTIONt_angle_deg1.4417643
X-RAY DIFFRACTIONt_dihedral_angle_d16.77690
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.006342
X-RAY DIFFRACTIONt_gen_planes0.0121845
X-RAY DIFFRACTIONt_it2.6413133
X-RAY DIFFRACTIONt_nbd0.0111310
Software
*PLUS
Name: TNT / Version: 5D / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.185 / Rfactor Rfree: 0.252
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 26.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_planar_d0.0062
X-RAY DIFFRACTIONt_plane_restr0.0125
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg16.70

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