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- PDB-7uv8: Rad6-Bre1 Complex -

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Basic information

Entry
Database: PDB / ID: 7uv8
TitleRad6-Bre1 Complex
Components
  • E3 ubiquitin-protein ligase BRE1
  • Ubiquitin-conjugating enzyme E2 2
KeywordsTRANSFERASE/LIGASE / E2 conjugation / 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 / HULC complex / error-free postreplication DNA repair / stress-induced homeostatically regulated protein degradation pathway / ubiquitin-dependent protein catabolic process via the N-end rule pathway / cytoplasm protein quality control by the ubiquitin-proteasome system ...MUB1-RAD6-UBR2 ubiquitin ligase complex / RAD6-UBR2 ubiquitin ligase complex / Rad6-Rad18 complex / regulation of dipeptide transport / UBR1-RAD6 ubiquitin ligase complex / HULC complex / error-free postreplication DNA repair / stress-induced homeostatically regulated protein degradation pathway / ubiquitin-dependent protein catabolic process via the N-end rule pathway / cytoplasm protein quality control by the ubiquitin-proteasome system / meiotic DNA double-strand break formation / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / E3 ubiquitin ligases ubiquitinate target proteins / telomere maintenance via recombination / mitotic intra-S DNA damage checkpoint signaling / regulation of DNA-templated DNA replication initiation / DNA duplex unwinding / E2 ubiquitin-conjugating enzyme / error-free translesion synthesis / sporulation resulting in formation of a cellular spore / proteasome binding / DNA replication origin binding / ubiquitin conjugating enzyme activity / Antigen processing: Ubiquitination & Proteasome degradation / protein K63-linked ubiquitination / subtelomeric heterochromatin formation / error-prone translesion synthesis / 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 / 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 / ATP binding / identical protein binding / nucleus / metal ion binding / 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, catalytic domain homologues / 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, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / 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 / SAD / Resolution: 2.7 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 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)66,8593
Polymers66,8593
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10990 Å2
ΔGint-101 kcal/mol
Surface area24090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)241.580, 49.951, 57.568
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: 17191.488 Da / Num. of mol.: 1
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: 2.6 Å3/Da / Density % sol: 52.65 %
Crystal growTemperature: 286.15 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: 80 K / Ambient temp details: 80 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2018 / Details: mirror
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.7→38.55 Å / Num. obs: 19967 / % possible obs: 100 % / Observed criterion σ(I): 20.9 / Redundancy: 37.72 % / Rsym value: 0.16 / Net I/σ(I): 20.9
Reflection shellResolution: 2.7→2.83 Å / Num. unique obs: 710 / Rsym value: 3.39 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
pointlessdata scaling
AMoREphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→38.49 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1007 5.04 %RANDOM
Rwork0.24 18960 --
obs0.242 19967 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 203.58 Å2 / Biso mean: 105.6 Å2 / Biso min: 53.11 Å2
Refinement stepCycle: final / Resolution: 2.7→38.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3861 0 0 0 3861
Num. residues----470
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7-2.840.4691360.445226472783
2.84-3.020.44041640.368926392803
3.02-3.250.34171290.323926472776
3.25-3.580.40111460.297827292875
3.58-4.10.2861300.240826802810
4.1-5.160.27371510.204627272878
5.16-38.490.1941510.186328913042
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.2827-1.17192.34672.2333-1.21682.8320.35910.0354-0.00510.0506-0.49261.1937-0.0076-0.7461-0.00970.62410.1503-0.07190.6894-0.19851.4095245.39462.094108.26
22.6684-0.59591.9150.0099-0.40942.62580.07290.26390.04170.0454-0.1940.1054-0.20440.13940.09140.83650.0645-0.04030.31650.04351.216287.50551.886134.533
33.349-0.51392.19270.6195-0.04433.08750.03940.18890.4340.0448-0.2110.0151-0.1711-0.12010.15770.65390.04960.07890.26890.02881.1381287.86356.683133.216
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:150 )A3 - 150
2X-RAY DIFFRACTION2( CHAIN V AND RESID 15:182 )V15 - 182
3X-RAY DIFFRACTION3( CHAIN U AND RESID 21:191 )U21 - 191

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