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- PDB-8btl: Crystal structure of a complex between the E2 conjugating enzyme ... -

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Basic information

Entry
Database: PDB / ID: 8btl
TitleCrystal structure of a complex between the E2 conjugating enzyme UBE2A and the E3 ligase module from UBR4
Components
  • Ubiquitin conjugating enzyme E2 A
  • cDNA FLJ12511 fis, clone NT2RM2001727, highly similar to Homo sapiens ubiquitin protein ligase E3 component n-recognin 4 (UBR4), mRNA
KeywordsLIGASE / E2 conjugating enzyme / E3 ligase / ubiquitin
Function / homology
Function and homology information


HULC complex / histone ubiquitin ligase activity / ubiquitin conjugating enzyme activity / ligase activity / response to UV / G2/M transition of mitotic cell cycle / DNA repair / ubiquitin protein ligase binding / ATP binding
Similarity search - Function
E3 ubiquitin ligase UBR4, C-terminal / E3 ubiquitin ligase UBR4-like / E3 ubiquitin-protein ligase UBR4 / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like
Similarity search - Domain/homology
Ubiquitin conjugating enzyme E2 A / cDNA FLJ12511 fis, clone NT2RM2001727, highly similar to Homo sapiens ubiquitin protein ligase E3 component n-recognin 4 (UBR4), mRNA
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsVirdee, S. / Mabbitt, P.D. / Barnsby-Greer, L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2024
Title: UBE2A and UBE2B are recruited by an atypical E3 ligase module in UBR4.
Authors: Barnsby-Greer, L. / Mabbitt, P.D. / Dery, M.A. / Squair, D.R. / Wood, N.T. / Lamoliatte, F. / Lange, S.M. / Virdee, S.
History
DepositionNov 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cDNA FLJ12511 fis, clone NT2RM2001727, highly similar to Homo sapiens ubiquitin protein ligase E3 component n-recognin 4 (UBR4), mRNA
C: Ubiquitin conjugating enzyme E2 A
D: Ubiquitin conjugating enzyme E2 A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7054
Polymers87,6403
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-0 kcal/mol
Surface area28490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.157, 89.157, 263.306
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein cDNA FLJ12511 fis, clone NT2RM2001727, highly similar to Homo sapiens ubiquitin protein ligase E3 component n-recognin 4 (UBR4), mRNA


Mass: 51755.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: B3KMT2
#2: Protein Ubiquitin conjugating enzyme E2 A


Mass: 17942.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2A / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7N4PN18
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.9 Å3/Da / Density % sol: 57.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 0.1 M Bis-Tris, pH 6.4, 15% PEG10000, 0.2 M Ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9118 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9118 Å / Relative weight: 1
ReflectionResolution: 3.2→65.83 Å / Num. obs: 18375 / % possible obs: 99.62 % / Redundancy: 12.5 % / CC1/2: 0.997 / CC star: 0.999 / Net I/σ(I): 8.04
Reflection shellResolution: 3.2→3.315 Å / Redundancy: 13.1 % / Mean I/σ(I) obs: 1.35 / Num. unique obs: 1813 / CC1/2: 0.934 / CC star: 0.983 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
DIALSdata reduction
DIALSdata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→65.83 Å / SU ML: 0.3894 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.3022
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2625 970 5.3 %
Rwork0.2282 17340 -
obs0.23 18310 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.05 Å2
Refinement stepCycle: LAST / Resolution: 3.2→65.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5186 0 1 0 5187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00175321
X-RAY DIFFRACTIONf_angle_d0.43987249
X-RAY DIFFRACTIONf_chiral_restr0.038794
X-RAY DIFFRACTIONf_plane_restr0.0038950
X-RAY DIFFRACTIONf_dihedral_angle_d15.5704711
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.370.33481410.30312389X-RAY DIFFRACTION99.49
3.37-3.580.31881380.26852426X-RAY DIFFRACTION99.57
3.58-3.860.26811320.25462430X-RAY DIFFRACTION99.65
3.86-4.240.30051470.23952454X-RAY DIFFRACTION99.77
4.24-4.860.22721440.20692444X-RAY DIFFRACTION99.69
4.86-6.120.25281220.23322520X-RAY DIFFRACTION99.77
6.12-65.830.23631460.1992677X-RAY DIFFRACTION99.58

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