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- PDB-7uvc: Rad6(P43L)-Bre1 Complex -

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Basic information

Entry
Database: PDB / ID: 7uvc
TitleRad6(P43L)-Bre1 Complex
Components
  • E3 ubiquitin-protein ligase BRE1
  • Ubiquitin-conjugating enzyme E2 2
KeywordsTRANSFERASE/LIGASE / Rad6 / E2 conjugating enzyme / Bre1 / E3-Ligase / LIGASE / TRANSFERASE-LIGASE complex
Function / homology
Function and homology information


MUB1-RAD6-UBR2 ubiquitin ligase complex / RAD6-UBR2 ubiquitin ligase complex / Rad6-Rad18 complex / regulation of dipeptide transport / UBR1-RAD6 ubiquitin ligase complex / sno(s)RNA transcription / HULC complex / error-free postreplication DNA repair / stress-induced homeostatically regulated protein degradation pathway / Synthesis of active ubiquitin: roles of E1 and E2 enzymes ...MUB1-RAD6-UBR2 ubiquitin ligase complex / RAD6-UBR2 ubiquitin ligase complex / Rad6-Rad18 complex / regulation of dipeptide transport / UBR1-RAD6 ubiquitin ligase complex / sno(s)RNA transcription / HULC complex / error-free postreplication DNA repair / stress-induced homeostatically regulated protein degradation pathway / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / meiotic DNA double-strand break formation / ubiquitin-dependent protein catabolic process via the N-end rule pathway / cytoplasm protein quality control by the ubiquitin-proteasome system / E3 ubiquitin ligases ubiquitinate target proteins / telomere maintenance via recombination / mitotic intra-S DNA damage checkpoint signaling / regulation of DNA-templated DNA replication initiation / E2 ubiquitin-conjugating enzyme / error-free translesion synthesis / sporulation resulting in formation of a cellular spore / proteasome binding / ubiquitin conjugating enzyme activity / Antigen processing: Ubiquitination & Proteasome degradation / DNA replication origin binding / cellular response to unfolded protein / error-prone translesion synthesis / subtelomeric heterochromatin formation / ERAD pathway / mitotic G1 DNA damage checkpoint signaling / DNA-templated transcription termination / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / scaffold protein binding / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription by RNA polymerase II / chromosome, telomeric region / protein ubiquitination / DNA repair / chromatin / zinc ion binding / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
E3 ubiquitin ligase Bre1 / BRE1 E3 ubiquitin ligase / : / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. ...E3 ubiquitin ligase Bre1 / BRE1 E3 ubiquitin ligase / : / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / 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 / Ring finger / Zinc finger C2H2-type / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 2 / E3 ubiquitin-protein ligase BRE1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsShukla, P.K. / Chandrasekharan, M.B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM127783 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)1R21HG011520-01 United States
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Structure and functional determinants of Rad6-Bre1 subunits in the histone H2B ubiquitin-conjugating complex.
Authors: Shukla, P.K. / Bissell, J.E. / Kumar, S. / Pokhrel, S. / Palani, S. / Radmall, K.S. / Obidi, O. / Parnell, T.J. / Brasch, J. / Shrieve, D.C. / Chandrasekharan, M.B.
History
DepositionApr 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 2
V: E3 ubiquitin-protein ligase BRE1
U: E3 ubiquitin-protein ligase BRE1


Theoretical massNumber of molelcules
Total (without water)66,8763
Polymers66,8763
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10850 Å2
ΔGint-99 kcal/mol
Surface area24510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)240.433, 50.088, 57.321
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 2 / E2 ubiquitin-conjugating enzyme 2 / Radiation sensitivity protein 6 / Ubiquitin carrier protein ...E2 ubiquitin-conjugating enzyme 2 / Radiation sensitivity protein 6 / Ubiquitin carrier protein UBC2 / Ubiquitin-protein ligase UBC2


Mass: 17207.531 Da / Num. of mol.: 1 / Mutation: P43L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: RAD6, UBC2, YGL058W / Plasmid: pRSF-Duet / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P06104, E2 ubiquitin-conjugating enzyme
#2: Protein E3 ubiquitin-protein ligase BRE1 / Brefeldin A-sensitivity protein 1 / RING-type E3 ubiquitin transferase BRE1


Mass: 24833.986 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: BRE1, YDL074C / Plasmid: pRSF-Duet / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q07457, RING-type E3 ubiquitin transferase

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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: 2.58 Å3/Da / Density % sol: 52.34 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 0.05 to 0.1 M MMT buffer and 15-25% PEG400

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 17, 2019 / Details: mirror
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.05→40 Å / Num. obs: 13829 / % possible obs: 99.9 % / Redundancy: 9.7 % / CC1/2: 0.999 / Rsym value: 0.2 / Net I/σ(I): 11.5
Reflection shellResolution: 3.05→3.26 Å / Redundancy: 9.4 % / Num. unique obs: 13829 / CC1/2: 0.674 / Rsym value: 2.79 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
pointlessdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7UV8

7uv8


Resolution: 3.05→37.72 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 37.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2789 693 5.01 %
Rwork0.2344 13136 -
obs0.2367 13829 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 223.7 Å2 / Biso mean: 126.6042 Å2 / Biso min: 67.13 Å2
Refinement stepCycle: final / Resolution: 3.05→37.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3864 0 0 0 3864
Num. residues----470
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 (%)
3.05-3.290.45771330.41742545267899
3.29-3.620.35211370.31082594273199
3.62-4.140.26381350.233625782713100
4.14-5.210.2561400.214626452785100
5.21-37.720.25211480.19382774292299
Refinement TLS params.Method: refined / Origin x: 273.1186 Å / Origin y: 57.092 Å / Origin z: 125.2036 Å
111213212223313233
T0.7158 Å20.0568 Å20.0613 Å2-0.5861 Å20.0076 Å2--1.3923 Å2
L3.1154 °2-0.7467 °22.0104 °2-0.8369 °2-0.3752 °2--2.2648 °2
S0.0838 Å °0.2309 Å °0.0971 Å °-0.0839 Å °-0.1751 Å °0.0946 Å °0.0064 Å °-0.2126 Å °0.0918 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 150
2X-RAY DIFFRACTION1allV15 - 182
3X-RAY DIFFRACTION1allU21 - 191

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