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- PDB-9en5: Crystal structure of yeast E2 Ubiquitin-conjugating enzyme Ubc6 U... -

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Basic information

Entry
Database: PDB / ID: 9en5
TitleCrystal structure of yeast E2 Ubiquitin-conjugating enzyme Ubc6 UBC domain
ComponentsUbiquitin-conjugating enzyme E2 6
KeywordsTRANSFERASE / Ubiquitin / Endoplasmic Reticulum / non-canonical ubiquitination
Function / homology
Function and homology information


Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / Antigen processing: Ubiquitination & Proteasome degradation / protein monoubiquitination / ERAD pathway / protein polyubiquitination / ubiquitin-protein transferase activity / endoplasmic reticulum membrane / endoplasmic reticulum ...Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / Antigen processing: Ubiquitination & Proteasome degradation / protein monoubiquitination / ERAD pathway / protein polyubiquitination / ubiquitin-protein transferase activity / endoplasmic reticulum membrane / endoplasmic reticulum / ATP binding / nucleus
Similarity search - Function
: / 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 6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsSwarnkar, A. / Stein, A.
Funding supportEuropean Union, Germany, 2items
OrganizationGrant numberCountry
European Research Council (ERC)677770European Union
German Research Foundation (DFG)SFB1190 P15 Germany
CitationJournal: Embo J. / Year: 2024
Title: Determinants of chemoselectivity in ubiquitination by the J2 family of ubiquitin-conjugating enzymes.
Authors: Swarnkar, A. / Leidner, F. / Rout, A.K. / Ainatzi, S. / Schmidt, C.C. / Becker, S. / Urlaub, H. / Griesinger, C. / Grubmuller, H. / Stein, A.
History
DepositionMar 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 25, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 6


Theoretical massNumber of molelcules
Total (without water)20,3471
Polymers20,3471
Non-polymers00
Water4,738263
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9240 Å2
Unit cell
Length a, b, c (Å)44.020, 55.384, 76.211
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 6 / E2 ubiquitin-conjugating enzyme 6 / Ubiquitin carrier protein UBC6 / Ubiquitin-protein ligase UBC6


Mass: 20347.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: UBC6, DOA2, YER100W / Production host: Escherichia coli (E. coli)
References: UniProt: P33296, E2 ubiquitin-conjugating enzyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, di-ammonium hydrogen citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.33→44.8 Å / Num. obs: 40931 / % possible obs: 94.15 % / Redundancy: 12.1 % / Biso Wilson estimate: 20.52 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.03871 / Rrim(I) all: 0.04035 / Net I/σ(I): 31.1
Reflection shellResolution: 1.33→1.378 Å / Rmerge(I) obs: 1.39 / Num. unique obs: 2752 / CC1/2: 0.67 / Rpim(I) all: 0.5561

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→44.8 Å / SU ML: 0.1915 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.7787
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1856 2041 4.99 %
Rwork0.1585 38872 -
obs0.1599 40913 94.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.31 Å2
Refinement stepCycle: LAST / Resolution: 1.33→44.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1368 0 0 263 1631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01181430
X-RAY DIFFRACTIONf_angle_d1.23881952
X-RAY DIFFRACTIONf_chiral_restr0.1041212
X-RAY DIFFRACTIONf_plane_restr0.0124252
X-RAY DIFFRACTIONf_dihedral_angle_d5.6043191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.33-1.360.6890.66161697X-RAY DIFFRACTION62.56
1.36-1.40.5121020.431930X-RAY DIFFRACTION72.26
1.4-1.430.33151190.28542248X-RAY DIFFRACTION82.07
1.43-1.480.26491350.19022572X-RAY DIFFRACTION94.35
1.48-1.520.20441430.1642718X-RAY DIFFRACTION99.97
1.52-1.580.19771440.16032715X-RAY DIFFRACTION99.97
1.58-1.640.22081420.17692715X-RAY DIFFRACTION99.93
1.64-1.720.21291430.16052711X-RAY DIFFRACTION99.93
1.72-1.810.20441430.13742748X-RAY DIFFRACTION100
1.81-1.920.18331450.13832761X-RAY DIFFRACTION99.97
1.92-2.070.1651440.14672734X-RAY DIFFRACTION100
2.07-2.280.17121450.13532769X-RAY DIFFRACTION100
2.28-2.60.16851460.14822794X-RAY DIFFRACTION100
2.6-3.280.16961480.15532808X-RAY DIFFRACTION100
3.28-44.80.17621530.15852952X-RAY DIFFRACTION99.9

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