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- PDB-5zb2: Crystal structure of Rad7 and Elc1 complex in yeast -

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Basic information

Entry
Database: PDB / ID: 5zb2
TitleCrystal structure of Rad7 and Elc1 complex in yeast
Components
  • DNA repair protein RAD7
  • Elongin-C
KeywordsDNA BINDING PROTEIN/LIGASE / LRR / ubiquitin ligase / complex / LIGASE / DNA BINDING PROTEIN-LIGASE complex
Function / homology
Function and homology information


nucleotide-excision repair factor 4 complex / protein localization => GO:0008104 / nucleotide-excision repair, DNA damage recognition / global genome nucleotide-excision repair / elongin complex / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul3-RING ubiquitin ligase complex / TP53 Regulates Transcription of DNA Repair Genes / Antigen processing: Ubiquitination & Proteasome degradation ...nucleotide-excision repair factor 4 complex / protein localization => GO:0008104 / nucleotide-excision repair, DNA damage recognition / global genome nucleotide-excision repair / elongin complex / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul3-RING ubiquitin ligase complex / TP53 Regulates Transcription of DNA Repair Genes / Antigen processing: Ubiquitination & Proteasome degradation / response to UV / nucleotide-excision repair / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / protein ubiquitination / cytoplasm
Similarity search - Function
Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / Elongin-C / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily ...Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / Elongin-C / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / Leucine-rich repeat domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-9FO / DNA repair protein RAD7 / Elongin-C
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.30000538295 Å
AuthorsJiang, T. / Liu, L. / Huo, Y.
CitationJournal: DNA Repair (Amst.) / Year: 2019
Title: Crystal structure of the yeast Rad7-Elc1 complex and assembly of the Rad7-Rad16-Elc1-Cul3 complex.
Authors: Liu, L. / Huo, Y. / Li, J. / Jiang, T.
History
DepositionFeb 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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: DNA repair protein RAD7
B: Elongin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,27212
Polymers57,1612
Non-polymers2,11110
Water4,234235
1
A: DNA repair protein RAD7
B: Elongin-C
hetero molecules

A: DNA repair protein RAD7
B: Elongin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,54524
Polymers114,3224
Non-polymers4,22320
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area15370 Å2
ΔGint-91 kcal/mol
Surface area40160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.921, 67.764, 69.015
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Components on special symmetry positions
IDModelComponents
11A-608-

P6G

21A-779-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein DNA repair protein RAD7


Mass: 45449.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RAD7, YJR052W, J1665 / Plasmid: pRSFDuet1 / Production host: Escherichia coli (E. coli) / References: UniProt: P06779
#2: Protein Elongin-C


Mass: 11712.006 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ELC1, YPL046C / Production host: Escherichia coli (E. coli) / References: UniProt: Q03071

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Non-polymers , 7 types, 245 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#5: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#6: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#7: Chemical ChemComp-9FO / 3,6,9,12,15,18,21,24,27,30,33,36,39,42,45,48,51,54,57-nonadecaoxanonapentacontane-1,59-diol


Mass: 899.066 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H82O21
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 0.1 M KCl, 0.1 M sodium Citrate tribasic dihydrate, 22% PEG 3350, 0.1 M Yttrium(III) cloride hexahydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 24237 / % possible obs: 97.5 % / Redundancy: 10.8 % / Biso Wilson estimate: 40.6194408749 Å2 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.035 / Rrim(I) all: 0.116 / Χ2: 1 / Net I/σ(I): 6.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.3411.70.68211860.8980.2030.7130.9596.3
2.34-2.3811.90.64711620.9110.190.6750.9496.4
2.38-2.4311.70.611710.9070.180.6270.97397.3
2.43-2.4811.60.55511700.9460.1670.5810.99195.8
2.48-2.5311.50.50111870.9310.1520.5251.01695.4
2.53-2.5911.40.42411780.9480.1280.4431.00297
2.59-2.6611.10.3711770.9660.1140.3881.02895.8
2.66-2.7310.60.3211950.9760.1010.3361.09496.8
2.73-2.819.90.26511990.9810.0870.2791.09798
2.81-2.99.80.23411970.9790.0780.2481.10597.4
2.9-310.50.21312170.9820.0680.2241.0999
3-3.1211.20.17812110.9880.0550.1861.02698.8
3.12-3.2610.60.1512360.9880.0490.1581.04499
3.26-3.44100.12612260.9910.0420.1341.04899.3
3.44-3.6511.40.10712390.9950.0330.1120.99299.1
3.65-3.937.90.09111510.9950.0330.0971.03692.1
3.93-4.3311.70.07512430.9970.0230.0780.87999.5
4.33-4.9510.10.06912540.9970.0230.0730.96498.1
4.95-6.2411.50.06612810.9970.0210.070.91899.3
6.24-5010.30.05713570.9960.020.0610.89898.7

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Processing

Software
NameVersionClassification
phenix.refine1.10_2155refinement
PHENIX1.10_2155refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.30000538295→48.3526115655 Å / SU ML: 0.253081575482 / Cross valid method: THROUGHOUT / σ(F): 1.35155306082 / Phase error: 23.2946347681
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.224072294486 1930 8.33225402582 %
Rwork0.194547878919 21233 -
obs0.197077370165 23163 97.4873737374 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.0157372333 Å2
Refinement stepCycle: LAST / Resolution: 2.30000538295→48.3526115655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3789 0 141 235 4165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003292115820923982
X-RAY DIFFRACTIONf_angle_d0.5297412962745335
X-RAY DIFFRACTIONf_chiral_restr0.0407692024212623
X-RAY DIFFRACTIONf_plane_restr0.00227910593722662
X-RAY DIFFRACTIONf_dihedral_angle_d17.80971034411538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.35750.267981014751330.2212705427651448X-RAY DIFFRACTION96.0510328068
2.3575-2.42130.2727348934551370.235812326991474X-RAY DIFFRACTION95.9499702204
2.4213-2.49250.3008176344141420.2286170208331470X-RAY DIFFRACTION96.991576414
2.4925-2.5730.2918713314671290.2245385786031482X-RAY DIFFRACTION96.7567567568
2.573-2.66490.2559801012641420.2064628081841482X-RAY DIFFRACTION96.5517241379
2.6649-2.77160.2643850652181330.2134748748581500X-RAY DIFFRACTION96.9714964371
2.7716-2.89770.2390637815631340.2063459860641501X-RAY DIFFRACTION98.0215827338
2.8977-3.05050.2030202332481340.2128208531611515X-RAY DIFFRACTION98.6834230999
3.0505-3.24160.2485718777081460.2061308526091532X-RAY DIFFRACTION98.9386792453
3.2416-3.49180.2576958439031370.1906394177541545X-RAY DIFFRACTION99.2330383481
3.4918-3.8430.2187899258881390.1785431241571482X-RAY DIFFRACTION94.3538998836
3.843-4.39880.1694209828891380.1582475834881553X-RAY DIFFRACTION99.1788856305
4.3988-5.54080.2218714163691330.1760721073041580X-RAY DIFFRACTION98.3917288914
5.5408-48.36330.2038353169691530.2106428617931669X-RAY DIFFRACTION98.7533875339

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