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- PDB-9gls: Crystal Structure of Human UBCH5B C85E -

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Basic information

Entry
Database: PDB / ID: 9gls
TitleCrystal Structure of Human UBCH5B C85E
ComponentsUbiquitin-conjugating enzyme E2 D2
KeywordsLIGASE / Ubiquitin conjugating protein / E2~UB thioester mimic
Function / homology
Function and homology information


(E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / protein autoubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / Negative regulators of DDX58/IFIH1 signaling ...(E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / protein autoubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / Negative regulators of DDX58/IFIH1 signaling / Peroxisomal protein import / Regulation of TNFR1 signaling / Inactivation of CSF3 (G-CSF) signaling / protein modification process / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / ubiquitin-dependent protein catabolic process / protein ubiquitination / protein-containing complex / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytosol
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
Ubiquitin-conjugating enzyme E2 D2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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: Ubiquitin-conjugating enzyme E2 D2


Theoretical massNumber of molelcules
Total (without water)16,8381
Polymers16,8381
Non-polymers00
Water2,162120
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)47.916, 49.401, 63.228
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 D2 / (E3-independent) E2 ubiquitin-conjugating enzyme D2 / E2 ubiquitin-conjugating enzyme D2 / ...(E3-independent) E2 ubiquitin-conjugating enzyme D2 / E2 ubiquitin-conjugating enzyme D2 / Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2(17)KB 2 / Ubiquitin-conjugating enzyme E2-17 kDa 2 / Ubiquitin-protein ligase D2 / p53-regulated ubiquitin-conjugating enzyme 1


Mass: 16838.250 Da / Num. of mol.: 1 / Mutation: C85E
Source method: isolated from a genetically manipulated source
Details: UBCH5B C85E / Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B / Production host: Escherichia coli (E. coli)
References: UniProt: P62837, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.22 Å3/Da / Density % sol: 44.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 10% PEG 200, 0.1 M Bis-Tris propane, pH 9, 15% PEG 8000

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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: 1.25→38.93 Å / Num. obs: 41718 / % possible obs: 98.75 % / Redundancy: 3.7 % / Biso Wilson estimate: 20.24 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.04743 / Net I/σ(I): 12.33
Reflection shellResolution: 1.25→1.295 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.35 / Num. unique obs: 4119 / CC1/2: 0.586 / Rrim(I) all: 0.9445 / % possible all: 98.59

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
CootWinCoot 0.9.6 ELmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→38.928 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.933 / SU ML: 0.04 / Cross valid method: FREE R-VALUE / ESU R: 0.049 / ESU R Free: 0.05
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2112 2054 4.924 %
Rwork0.1885 39663 -
all0.189 --
obs-41717 98.752 %
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: 21.687 Å2
Baniso -1Baniso -2Baniso -3
1-0.134 Å2-0 Å2-0 Å2
2---0.315 Å20 Å2
3---0.181 Å2
Refinement stepCycle: LAST / Resolution: 1.25→38.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1168 0 0 120 1288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0131319
X-RAY DIFFRACTIONr_bond_other_d0.0080.0151194
X-RAY DIFFRACTIONr_angle_refined_deg1.8421.6511820
X-RAY DIFFRACTIONr_angle_other_deg1.6671.5772781
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6375174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2922.31969
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.45615208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.236158
X-RAY DIFFRACTIONr_chiral_restr0.10.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021560
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02308
X-RAY DIFFRACTIONr_nbd_refined0.2210.2263
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.21043
X-RAY DIFFRACTIONr_nbtor_refined0.180.2631
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.2532
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.284
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1730.211
X-RAY DIFFRACTIONr_nbd_other0.2760.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1810.217
X-RAY DIFFRACTIONr_mcbond_it1.7152.006645
X-RAY DIFFRACTIONr_mcbond_other1.6932.004644
X-RAY DIFFRACTIONr_mcangle_it2.4143.013821
X-RAY DIFFRACTIONr_mcangle_other2.4243.015822
X-RAY DIFFRACTIONr_scbond_it3.432.379674
X-RAY DIFFRACTIONr_scbond_other3.4162.378674
X-RAY DIFFRACTIONr_scangle_it4.7883.431994
X-RAY DIFFRACTIONr_scangle_other4.7823.431994
X-RAY DIFFRACTIONr_lrange_it5.64625.6181504
X-RAY DIFFRACTIONr_lrange_other5.60125.1631481
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.25-1.2820.3411560.32428740.32530750.7370.74298.53660.321
1.282-1.3180.3651310.31128410.31330110.7510.79798.70480.304
1.318-1.3560.3311480.27327310.27629080.8020.83599.00270.263
1.356-1.3970.2511400.25326690.25328330.8680.86599.15280.236
1.397-1.4430.2581070.23626250.23727670.90.89698.73510.217
1.443-1.4940.2311380.20524940.20726640.9190.9398.79880.186
1.494-1.550.2141510.19624110.19725760.9330.94299.45650.179
1.55-1.6130.2111280.20223400.20224810.9360.93599.4760.185
1.613-1.6850.2161150.19822420.19923710.9350.93799.40950.185
1.685-1.7670.2471290.19521900.19823250.930.94299.74190.183
1.767-1.8620.2281160.18820330.1921580.9350.9599.58290.182
1.862-1.9750.191210.18219360.18220700.950.95399.3720.186
1.975-2.1110.204800.18518410.18619370.9410.95299.1740.196
2.111-2.2790.214870.17717180.17818290.9450.95598.68780.199
2.279-2.4960.227730.18215620.18316830.9420.95497.14790.208
2.496-2.7890.21630.18314360.18415210.9450.95698.55360.218
2.789-3.2180.161650.18712820.18613730.9620.95198.10630.234
3.218-3.9350.246480.17710860.17911650.9470.96697.33910.229
3.935-5.5360.171410.1538540.1539290.9740.97896.34010.212
5.536-38.9280.191170.224980.2195680.9610.95890.6690.318

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