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- PDB-9glt: Crystal Structure of Yeast Ubc13 C87E -

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Basic information

Entry
Database: PDB / ID: 9glt
TitleCrystal Structure of Yeast Ubc13 C87E
ComponentsUbiquitin-conjugating enzyme E2 13
KeywordsLIGASE / Ubiquitin conjugating protein E2 UBC13~UB thioester complex mimic
Function / homology
Function and homology information


protein targeting to vacuolar membrane / Interleukin-1 signaling / Aggrephagy / PINK1-PRKN Mediated Mitophagy / ubiquitin conjugating enzyme complex / free ubiquitin chain polymerization / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / fungal-type vacuole membrane / DNA damage tolerance ...protein targeting to vacuolar membrane / Interleukin-1 signaling / Aggrephagy / PINK1-PRKN Mediated Mitophagy / ubiquitin conjugating enzyme complex / free ubiquitin chain polymerization / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / fungal-type vacuole membrane / DNA damage tolerance / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / Antigen processing: Ubiquitination & Proteasome degradation / protein K63-linked ubiquitination / protein polyubiquitination / ATP binding / nucleus / cytoplasm / 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 13
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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

Downloads & links

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Assembly

Deposited unit
AAA: Ubiquitin-conjugating enzyme E2 13
BBB: Ubiquitin-conjugating enzyme E2 13


Theoretical massNumber of molelcules
Total (without water)35,1462
Polymers35,1462
Non-polymers00
Water5,260292
1
AAA: Ubiquitin-conjugating enzyme E2 13


Theoretical massNumber of molelcules
Total (without water)17,5731
Polymers17,5731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Ubiquitin-conjugating enzyme E2 13


Theoretical massNumber of molelcules
Total (without water)17,5731
Polymers17,5731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.603, 127.663, 42.330
Angle α, β, γ (deg.)90.000, 96.210, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 13 / E2 ubiquitin-conjugating enzyme 13 / Ubiquitin carrier protein 13 / Ubiquitin-protein ligase 13


Mass: 17573.008 Da / Num. of mol.: 2 / Mutation: C87E
Source method: isolated from a genetically manipulated source
Details: UBC13 C87E Chain A
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: UBC13, YDR092W, YD6652.04 / Production host: Escherichia coli (E. coli)
References: UniProt: P52490, E2 ubiquitin-conjugating enzyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 1.96 Å3/Da / Density % sol: 37.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M sodium cacodylate, pH 6.5, 25% PEG 4000

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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: 1.45→42.08 Å / Num. obs: 46789 / % possible obs: 98.06 % / Redundancy: 2.8 % / Biso Wilson estimate: 16.26 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.065 / Net I/σ(I): 11.87
Reflection shellResolution: 1.45→1.502 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4758 / CC1/2: 0.737 / Rrim(I) all: 0.5799 / % possible all: 99.69

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
CootWinCoot 0.9.6 ELmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→42.08 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.511 / SU ML: 0.059 / Cross valid method: FREE R-VALUE / ESU R: 0.08 / ESU R Free: 0.083
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.228 2339 5.004 %
Rwork0.1913 44406 -
all0.193 --
obs-46745 98.074 %
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: 17.453 Å2
Baniso -1Baniso -2Baniso -3
1-0.128 Å2-0 Å20.148 Å2
2---0.103 Å2-0 Å2
3----0.056 Å2
Refinement stepCycle: LAST / Resolution: 1.45→42.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2366 0 0 292 2658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132450
X-RAY DIFFRACTIONr_bond_other_d0.0030.0152329
X-RAY DIFFRACTIONr_angle_refined_deg1.7581.6543349
X-RAY DIFFRACTIONr_angle_other_deg1.491.5765391
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4025300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14823.226124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.66215414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7461514
X-RAY DIFFRACTIONr_chiral_restr0.0920.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022737
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02507
X-RAY DIFFRACTIONr_nbd_refined0.2310.2524
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2140.22199
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21217
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.21099
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2179
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3610.219
X-RAY DIFFRACTIONr_nbd_other0.2740.287
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2190.230
X-RAY DIFFRACTIONr_mcbond_it1.6721.5781200
X-RAY DIFFRACTIONr_mcbond_other1.6711.5761199
X-RAY DIFFRACTIONr_mcangle_it2.4162.3631500
X-RAY DIFFRACTIONr_mcangle_other2.4152.3641501
X-RAY DIFFRACTIONr_scbond_it2.7721.8941250
X-RAY DIFFRACTIONr_scbond_other2.7711.8951251
X-RAY DIFFRACTIONr_scangle_it4.0772.7251849
X-RAY DIFFRACTIONr_scangle_other4.0762.7271850
X-RAY DIFFRACTIONr_lrange_it5.47520.4472853
X-RAY DIFFRACTIONr_lrange_other5.34119.8562787
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.4880.2821770.2533341X-RAY DIFFRACTION99.7448
1.488-1.5280.2611780.243242X-RAY DIFFRACTION99.5923
1.528-1.5730.2561760.2293138X-RAY DIFFRACTION99.4299
1.573-1.6210.2751550.2163089X-RAY DIFFRACTION99.4177
1.621-1.6740.2531620.2052909X-RAY DIFFRACTION98.8095
1.674-1.7330.2521560.2032852X-RAY DIFFRACTION99.5038
1.733-1.7980.2461440.1972773X-RAY DIFFRACTION99.3529
1.798-1.8720.2711400.2012633X-RAY DIFFRACTION98.8944
1.872-1.9550.2591170.2022569X-RAY DIFFRACTION98.2084
1.955-2.050.2151200.1952408X-RAY DIFFRACTION98.6344
2.05-2.1610.2471270.1912307X-RAY DIFFRACTION97.6334
2.161-2.2920.215980.1852139X-RAY DIFFRACTION97.1764
2.292-2.450.226950.1822055X-RAY DIFFRACTION97.5942
2.45-2.6460.2171080.1731854X-RAY DIFFRACTION96.1293
2.646-2.8980.22940.1981717X-RAY DIFFRACTION96.5867
2.898-3.2390.232810.1841535X-RAY DIFFRACTION93.7899
3.239-3.7380.204740.1761352X-RAY DIFFRACTION95.7047
3.738-4.5750.2600.1521124X-RAY DIFFRACTION94.4179
4.575-6.4530.184500.199890X-RAY DIFFRACTION93.1615
6.453-42.080.227270.21478X-RAY DIFFRACTION92.6606

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