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- PDB-6cyo: Crystal structure of human UBE2A (RAD6A) -

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Basic information

Entry
Database: PDB / ID: 6cyo
TitleCrystal structure of human UBE2A (RAD6A)
ComponentsUbiquitin-conjugating enzyme E2 A
KeywordsLIGASE / TRANSFERASE / Ubiquitin-Conjungating enzyme E2 A
Function / homology
Function and homology information


HULC complex / histone ubiquitin ligase activity / protein K11-linked ubiquitination / postreplication repair / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / response to UV / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ubiquitin binding ...HULC complex / histone ubiquitin ligase activity / protein K11-linked ubiquitination / postreplication repair / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / response to UV / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ubiquitin binding / protein polyubiquitination / ubiquitin-protein transferase activity / G2/M transition of mitotic cell cycle / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / chromatin remodeling / DNA repair / ubiquitin protein ligase binding / chromatin / nucleoplasm / ATP binding / cytosol
Similarity search - Function
Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsRanzani, A.T. / de Oliveira, J.F.
CitationJournal: Nat. Chem. Biol. / Year: 2019
Title: Mechanistic insights revealed by a UBE2A mutation linked to intellectual disability.
Authors: de Oliveira, J.F. / do Prado, P.F.V. / da Costa, S.S. / Sforca, M.L. / Canateli, C. / Ranzani, A.T. / Maschietto, M. / de Oliveira, P.S.L. / Otto, P.A. / Klevit, R.E. / Krepischi, A.C.V. / ...Authors: de Oliveira, J.F. / do Prado, P.F.V. / da Costa, S.S. / Sforca, M.L. / Canateli, C. / Ranzani, A.T. / Maschietto, M. / de Oliveira, P.S.L. / Otto, P.A. / Klevit, R.E. / Krepischi, A.C.V. / Rosenberg, C. / Franchini, K.G.
History
DepositionApr 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 A


Theoretical massNumber of molelcules
Total (without water)17,6151
Polymers17,6151
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.497, 51.350, 88.663
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 A / E2 ubiquitin-conjugating enzyme A / RAD6 homolog A / hHR6A / Ubiquitin carrier protein A / ...E2 ubiquitin-conjugating enzyme A / RAD6 homolog A / hHR6A / Ubiquitin carrier protein A / Ubiquitin-protein ligase A


Mass: 17614.643 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2A, RAD6A / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta II(DE3)
References: UniProt: P49459, E2 ubiquitin-conjugating enzyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.46 Å3/Da / Density % sol: 49.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 50 mM di-Sodium succinate pH 7.0 and 12-14% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45863 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45863 Å / Relative weight: 1
ReflectionResolution: 1.85→44.44 Å / Num. obs: 15168 / % possible obs: 99.4 % / Redundancy: 11.4 % / Biso Wilson estimate: 36.75 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.019 / Rrim(I) all: 0.067 / Net I/σ(I): 18.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.85-1.898.71.6929100.6020.6011.80298.3
9.06-44.449.60.041640.9980.0130.04299.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.21data scaling
MOLREPphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YB6

2yb6


Resolution: 1.85→28.657 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.24
RfactorNum. reflection% reflection
Rfree0.214 728 4.82 %
Rwork0.204 --
obs0.2045 15115 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.56 Å2 / Biso mean: 46.4198 Å2 / Biso min: 24.27 Å2
Refinement stepCycle: final / Resolution: 1.85→28.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1222 0 0 72 1294
Biso mean---51.52 -
Num. residues----152
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.99280.2951330.27282746287997
1.9928-2.19330.27171660.231628373003100
2.1933-2.51050.28531270.234828712998100
2.5105-3.16240.26561320.239629223054100
3.1624-28.66060.17551700.17630113181100
Refinement TLS params.Method: refined / Origin x: 9.4922 Å / Origin y: -3.8424 Å / Origin z: 19.9134 Å
111213212223313233
T0.229 Å20.001 Å2-0.0217 Å2-0.2039 Å20.002 Å2--0.3045 Å2
L3.3205 °2-0.9972 °2-2.3283 °2-1.7479 °21.0833 °2--5.0036 °2
S0.1156 Å °-0.0589 Å °0.2963 Å °0.0465 Å °-0.0276 Å °-0.0071 Å °-0.2699 Å °0.0801 Å °-0.0876 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA0 - 151
2X-RAY DIFFRACTION1allS1 - 73

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