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- PDB-4r62: Structure of Rad6~Ub -

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Basic information

Entry
Database: PDB / ID: 4r62
TitleStructure of Rad6~Ub
Components
  • Ubiquitin-40S ribosomal protein S27a
  • Ubiquitin-conjugating enzyme E2 2
KeywordsNUCLEAR PROTEIN / E2 conjugating enzyme / UBC / Monoubiquitination of Histone H2B at K123 in Saccharomyces cerevisiae / Bre1 / Ubiquitin / PCNA / Rad18 / Histone H2B / UBIQUITINATION / NUCLEUS
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 / error-free postreplication DNA repair / HULC complex / stress-induced homeostatically regulated protein degradation pathway / ubiquitin-dependent protein catabolic process via the N-end rule pathway / meiotic DNA double-strand break formation ...MUB1-RAD6-UBR2 ubiquitin ligase complex / RAD6-UBR2 ubiquitin ligase complex / Rad6-Rad18 complex / regulation of dipeptide transport / UBR1-RAD6 ubiquitin ligase complex / error-free postreplication DNA repair / HULC complex / stress-induced homeostatically regulated protein degradation pathway / ubiquitin-dependent protein catabolic process via the N-end rule pathway / meiotic DNA double-strand break formation / cytoplasm protein quality control by the ubiquitin-proteasome system / telomere maintenance via recombination / Formation of the ternary complex, and subsequently, the 43S complex / E2 ubiquitin-conjugating enzyme / DNA duplex unwinding / Ribosomal scanning and start codon recognition / Translation initiation complex formation / error-free translesion synthesis / sporulation resulting in formation of a cellular spore / proteasome binding / SARS-CoV-1 modulates host translation machinery / ubiquitin conjugating enzyme activity / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / subtelomeric heterochromatin formation / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / error-prone translesion synthesis / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / : / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / mitotic G1 DNA damage checkpoint signaling / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / small-subunit processome / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / cytosolic ribosome / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1
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. / S27a-like superfamily / Ubiquitin-conjugating enzyme/RWD-like ...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. / S27a-like superfamily / Ubiquitin-conjugating enzyme/RWD-like / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Zinc-binding ribosomal protein / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Ubiquitin-conjugating enzyme E2 2 / Ubiquitin-ribosomal protein eS31 fusion protein
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsKumar, P. / Wolberger, C.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Role of a non-canonical surface of Rad6 in ubiquitin conjugating activity.
Authors: Kumar, P. / Magala, P. / Geiger-Schuller, K.R. / Majumdar, A. / Tolman, J.R. / Wolberger, C.
History
DepositionAug 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 2
B: Ubiquitin-40S ribosomal protein S27a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6293
Polymers28,5702
Non-polymers591
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.666, 58.412, 115.722
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 19751.699 Da / Num. of mol.: 1 / Fragment: Rad6 / Mutation: C88K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RAD6, UBC2, YGL058W / Plasmid: pMALc2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 DE3 pLysS / References: UniProt: P06104, ubiquitin-protein ligase
#2: Protein Ubiquitin-40S ribosomal protein S27a / Ubiquitin carboxyl extension protein 80 / Ubiquitin / 40S ribosomal protein S27a


Mass: 8818.117 Da / Num. of mol.: 1 / Fragment: Ubiquitin
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: human / Gene: RPS27A, UBA80, UBCEP1, Ubiquitin / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 DE3 pLysS / References: UniProt: P62979
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 1.99 Å3/Da / Density % sol: 38.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 24% PEG 300, 50 mM sodium acetate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03 Å
DetectorType: PILATUS3 6M / Detector: PIXEL / Date: Aug 10, 2014 / Details: Silicon sensor
RadiationMonochromator: Silicon sensor / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 20019 / Num. obs: 11656 / % possible obs: 96.5 % / Redundancy: 2.9 % / Biso Wilson estimate: 59.83 Å2 / Rmerge(I) obs: 0.106 / Rsym value: 0.104 / Net I/σ(I): 2.15

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AYZ and 1UBQ

1ayz

1ubq


Resolution: 2.28→41.107 Å / SU ML: 0.35 / σ(F): 1.34 / Phase error: 34.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2645 534 4.99 %
Rwork0.2101 --
obs0.2128 10705 97.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.28→41.107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1719 0 4 12 1735
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011764
X-RAY DIFFRACTIONf_angle_d1.1942409
X-RAY DIFFRACTIONf_dihedral_angle_d14.56633
X-RAY DIFFRACTIONf_chiral_restr0.074279
X-RAY DIFFRACTIONf_plane_restr0.006315
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.50950.37991270.29812431X-RAY DIFFRACTION96
2.5095-2.87250.37381340.25872552X-RAY DIFFRACTION99
2.8725-3.61870.29561360.24052549X-RAY DIFFRACTION99
3.6187-41.1140.22741370.1832639X-RAY DIFFRACTION96

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