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- PDB-5ojw: S. cerevisiae UBC13 - MMs2 complex -

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Basic information

Entry
Database: PDB / ID: 5ojw
TitleS. cerevisiae UBC13 - MMs2 complex
Components
  • Ubiquitin-conjugating enzyme E2 13
  • Ubiquitin-conjugating enzyme variant MMS2
KeywordsSIGNALING PROTEIN / E2 / Ubiquitin / complex
Function / homology
Function and homology information


protein targeting to vacuolar membrane / PINK1-PRKN Mediated Mitophagy / Interleukin-1 signaling / Aggrephagy / 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 / postreplication repair ...protein targeting to vacuolar membrane / PINK1-PRKN Mediated Mitophagy / Interleukin-1 signaling / Aggrephagy / 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 / postreplication repair / E2 ubiquitin-conjugating enzyme / ligase activity / ubiquitin conjugating enzyme activity / Antigen processing: Ubiquitination & Proteasome degradation / protein K63-linked ubiquitination / protein polyubiquitination / 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 / 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 13 / Ubiquitin-conjugating enzyme variant MMS2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSharon, I. / Rathi, R. / Levin-Kravets, O. / Attali, I. / Prag, G.
CitationJournal: To Be Published
Title: S. cerevisiae UBC13 - MMs2 complex
Authors: Sharon, I. / Rathi, R. / Levin-Kravets, O. / Attali, I. / Prag, G.
History
DepositionJul 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 13
B: Ubiquitin-conjugating enzyme variant MMS2


Theoretical massNumber of molelcules
Total (without water)32,9272
Polymers32,9272
Non-polymers00
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-7 kcal/mol
Surface area15050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.425, 66.281, 126.614
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 17360.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: UBC13, YDR092W, YD6652.04 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P52490, E2 ubiquitin-conjugating enzyme
#2: Protein Ubiquitin-conjugating enzyme variant MMS2 / UEV MMS2


Mass: 15565.644 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: MMS2, YGL087C / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P53152
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.32 Å3/Da / Density % sol: 47 % / Description: 1-2 mm long needles
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 0.1M Bis-Tris Propane / Citric Acid Buffer, pH 7.6, 20% PEG3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.070989 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.070989 Å / Relative weight: 1
ReflectionResolution: 1.773→45.78 Å / Num. obs: 29813 / % possible obs: 97.6 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.056 / Net I/σ(I): 11.1
Reflection shellResolution: 1.773→1.82 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JAT

1jat


Resolution: 2→45.78 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.35
RfactorNum. reflection% reflection
Rfree0.2054 1029 4.9 %
Rwork0.1603 --
obs0.1626 20979 97.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→45.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2314 0 0 246 2560
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112523
X-RAY DIFFRACTIONf_angle_d1.0353450
X-RAY DIFFRACTIONf_dihedral_angle_d20.3971595
X-RAY DIFFRACTIONf_chiral_restr0.057371
X-RAY DIFFRACTIONf_plane_restr0.008460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.10540.27391420.20762786X-RAY DIFFRACTION98
2.1054-2.23740.2451270.17292798X-RAY DIFFRACTION98
2.2374-2.41010.19881510.15892822X-RAY DIFFRACTION98
2.4101-2.65260.26321500.16112834X-RAY DIFFRACTION98
2.6526-3.03640.2081540.16292834X-RAY DIFFRACTION97
3.0364-3.82520.17811480.14462863X-RAY DIFFRACTION98
3.8252-45.79210.18431570.15833013X-RAY DIFFRACTION97

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