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- PDB-9glr: Crystal Structure of Human UBC9 C93E -

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Basic information

Entry
Database: PDB / ID: 9glr
TitleCrystal Structure of Human UBC9 C93E
ComponentsSUMO-conjugating enzyme UBC9
KeywordsLIGASE / SUMO-1 conjugating enzyme / Ubiquitin conjugating protein / SUMOLYATION Pathway protein / E2~SUMO thioester complex mimic
Function / homology
Function and homology information


: / SUMO conjugating enzyme activity / RING-like zinc finger domain binding / SUMO ligase complex / transferase complex / SUMOylation of nuclear envelope proteins / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / mitotic nuclear membrane reassembly ...: / SUMO conjugating enzyme activity / RING-like zinc finger domain binding / SUMO ligase complex / transferase complex / SUMOylation of nuclear envelope proteins / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / mitotic nuclear membrane reassembly / synaptonemal complex / small protein activating enzyme binding / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / SUMOylation of SUMOylation proteins / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / nuclear export / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / SUMOylation of ubiquitinylation proteins / transcription factor binding / SUMOylation of transcription factors / protein sumoylation / SUMOylation of DNA replication proteins / nuclear pore / SUMOylation of DNA damage response and repair proteins / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Transcriptional and post-translational regulation of MITF-M expression and activity / Meiotic synapsis / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / transcription coregulator binding / Regulation of endogenous retroelements by KRAB-ZFP proteins / chromosome segregation / SUMOylation of intracellular receptors / PKR-mediated signaling / protein modification process / PML body / Formation of Incision Complex in GG-NER / nuclear envelope / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Processing of DNA double-strand break ends / ubiquitin-dependent protein catabolic process / positive regulation of cell migration / cell division / negative regulation of DNA-templated transcription / perinuclear region of cytoplasm / enzyme binding / negative regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / 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
Similarity search - Domain/homology
SUMO-conjugating enzyme UBC9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsKumar, M. / Banerjee, S. / Wiener, R.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation491/2021 Israel
CitationJournal: Nat Commun / Year: 2025
Title: UFC1 reveals the multifactorial and plastic nature of oxyanion holes in E2 conjugating enzymes.
Authors: Kumar, M. / Banerjee, S. / Cohen-Kfir, E. / Mitelberg, M.B. / Tiwari, S. / Isupov, M.N. / Dessau, M. / Wiener, R.
History
DepositionAug 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 7, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: SUMO-conjugating enzyme UBC9


Theoretical massNumber of molelcules
Total (without water)18,1141
Polymers18,1141
Non-polymers00
Water2,414134
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.503, 96.650, 109.578
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein SUMO-conjugating enzyme UBC9 / RING-type E3 SUMO transferase UBC9 / SUMO-protein ligase / Ubiquitin carrier protein 9 / Ubiquitin ...RING-type E3 SUMO transferase UBC9 / SUMO-protein ligase / Ubiquitin carrier protein 9 / Ubiquitin carrier protein I / Ubiquitin-conjugating enzyme E2 I / Ubiquitin-protein ligase I / p18


Mass: 18113.836 Da / Num. of mol.: 1 / Mutation: C93E
Source method: isolated from a genetically manipulated source
Details: Ubiquitin conjugating enzyme UBC9 C93E mutant / Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2I, UBC9, UBCE9 / Production host: Escherichia coli (E. coli)
References: UniProt: P63279, Transferases; Acyltransferases; Aminoacyltransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.52 Å3/Da / Density % sol: 51.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 2% tacsimate, pH 5.0, 0.1 M sodium citrate, 16% PEG 3350

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.87313 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.72→48.33 Å / Num. obs: 19263 / % possible obs: 96.55 % / Redundancy: 1.9 % / Biso Wilson estimate: 31.99 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.03379 / Net I/σ(I): 12.65
Reflection shellResolution: 1.72→1.782 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.31 / Num. unique obs: 1914 / CC1/2: 0.645 / Rrim(I) all: 0.6958 / % possible all: 98.71

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
CootWinCoot 0.9.6 ELmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→48.33 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.183 / SU ML: 0.098 / Cross valid method: FREE R-VALUE / ESU R: 0.116 / ESU R Free: 0.111
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.227 964 5.004 %
Rwork0.1988 18299 -
all0.2 --
obs-19263 96.561 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 33.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.762 Å20 Å20 Å2
2---1.661 Å2-0 Å2
3---0.899 Å2
Refinement stepCycle: LAST / Resolution: 1.72→48.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1247 0 0 134 1381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131296
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151215
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.6581763
X-RAY DIFFRACTIONr_angle_other_deg1.3151.5772811
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4175158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.97122.35368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8315215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.454159
X-RAY DIFFRACTIONr_chiral_restr0.0820.2164
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021464
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02295
X-RAY DIFFRACTIONr_nbd_refined0.2190.2261
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.21110
X-RAY DIFFRACTIONr_nbtor_refined0.170.2605
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.2544
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.284
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0110.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1760.23
X-RAY DIFFRACTIONr_nbd_other0.20.224
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1640.210
X-RAY DIFFRACTIONr_mcbond_it2.653.296631
X-RAY DIFFRACTIONr_mcbond_other2.6383.296631
X-RAY DIFFRACTIONr_mcangle_it3.684.926789
X-RAY DIFFRACTIONr_mcangle_other3.6824.933790
X-RAY DIFFRACTIONr_scbond_it3.8253.612665
X-RAY DIFFRACTIONr_scbond_other3.7843.614665
X-RAY DIFFRACTIONr_scangle_it5.6885.251974
X-RAY DIFFRACTIONr_scangle_other5.685.252974
X-RAY DIFFRACTIONr_lrange_it7.15539.0761471
X-RAY DIFFRACTIONr_lrange_other7.11738.6881446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.7650.359650.3681346X-RAY DIFFRACTION98.3275
1.765-1.8130.317560.3131343X-RAY DIFFRACTION98.4518
1.813-1.8660.298680.2911282X-RAY DIFFRACTION98.7564
1.866-1.9230.339630.2581261X-RAY DIFFRACTION97.7122
1.923-1.9860.323640.2471209X-RAY DIFFRACTION99.3755
1.986-2.0560.259540.2181190X-RAY DIFFRACTION97.5686
2.056-2.1330.234490.2091122X-RAY DIFFRACTION96.8569
2.133-2.220.229620.2011072X-RAY DIFFRACTION97.9275
2.22-2.3190.272630.2021050X-RAY DIFFRACTION97.8032
2.319-2.4320.252620.203993X-RAY DIFFRACTION97.5948
2.432-2.5640.193470.186943X-RAY DIFFRACTION96.3973
2.564-2.7190.239440.197904X-RAY DIFFRACTION96.8335
2.719-2.9070.257430.212839X-RAY DIFFRACTION95.8696
2.907-3.1390.199480.201778X-RAY DIFFRACTION95.1613
3.139-3.4390.212440.191713X-RAY DIFFRACTION94.5069
3.439-3.8440.239360.171641X-RAY DIFFRACTION93.5083
3.844-4.4380.191390.152543X-RAY DIFFRACTION90.3727
4.438-5.4330.193280.156483X-RAY DIFFRACTION91.7415
5.433-7.6740.222200.225372X-RAY DIFFRACTION89.2938
7.674-38.930.13690.209216X-RAY DIFFRACTION83.0258

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