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- PDB-2y43: Rad18 ubiquitin ligase RING domain structure -

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Basic information

Entry
Database: PDB / ID: 2y43
TitleRad18 ubiquitin ligase RING domain structure
ComponentsE3 UBIQUITIN-PROTEIN LIGASE RAD18
KeywordsLIGASE / DNA REPAIR / METAL-BINDING / TRANSLESION SYNTHESIS / UBL CONJUGATION PATHWAY
Function / homology
Function and homology information


Rad6-Rad18 complex / positive regulation of chromosome segregation / Y-form DNA binding / nuclear inclusion body / postreplication repair / molecular function inhibitor activity / protein monoubiquitination / polyubiquitin modification-dependent protein binding / protein autoubiquitination / replication fork ...Rad6-Rad18 complex / positive regulation of chromosome segregation / Y-form DNA binding / nuclear inclusion body / postreplication repair / molecular function inhibitor activity / protein monoubiquitination / polyubiquitin modification-dependent protein binding / protein autoubiquitination / replication fork / Recognition of DNA damage by PCNA-containing replication complex / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / single-stranded DNA binding / E3 ubiquitin ligases ubiquitinate target proteins / site of double-strand break / damaged DNA binding / nuclear body / DNA repair / centrosome / DNA damage response / ubiquitin protein ligase binding / protein-containing complex binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase Rad18 / Rad18-like CCHC zinc finger / Zinc finger, C3HC4 type (RING finger) / SAP domain superfamily / SAP domain / SAP motif profile. / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. ...E3 ubiquitin-protein ligase Rad18 / Rad18-like CCHC zinc finger / Zinc finger, C3HC4 type (RING finger) / SAP domain superfamily / SAP domain / SAP motif profile. / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RAD18
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsHibbert, R.G. / Sixma, T.K.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Symmetry and Asymmetry of the Ring-Ring Dimer of Rad18.
Authors: Huang, A. / Hibbert, R.G. / De Jong, R.N. / Das, D. / Sixma, T.K. / Boelens, R.
History
DepositionJan 4, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 UBIQUITIN-PROTEIN LIGASE RAD18
B: E3 UBIQUITIN-PROTEIN LIGASE RAD18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0146
Polymers22,7532
Non-polymers2624
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-34.7 kcal/mol
Surface area9750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.646, 29.357, 69.736
Angle α, β, γ (deg.)90.00, 125.05, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein E3 UBIQUITIN-PROTEIN LIGASE RAD18 / RAD18 / POSTREPLICATION REPAIR PROTEIN RAD18 / RING FINGER PROTEIN 73 / HHR18 / HRAD18


Mass: 11376.327 Da / Num. of mol.: 2 / Fragment: RING DOMAIN, RESIDUES 1-99
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9NS91, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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 Å3/Da / Density % sol: 38 % / Description: NONE
Crystal growpH: 5.5
Details: 15% PEG 3350, 100 MM AMMONIUM ACETATE, 100 MM BIS-TRIS PH 5.5 .

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.2828
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2828 Å / Relative weight: 1
ReflectionResolution: 1.8→42.84 Å / Num. obs: 16560 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 17.3 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 24.3
Reflection shellResolution: 1.8→1.89 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.5 / % possible all: 99.2

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALAdata scaling
SHELXphasing
PHASERphasing
REFMAC5.5.0099refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.8→42.86 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.874 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22311 828 5 %RANDOM
Rwork0.17505 ---
obs0.1774 15732 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.531 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å20.27 Å2
2---0.04 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.8→42.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1421 0 4 102 1527
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221452
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2071.971968
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1225174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69123.49263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43115262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1931510
X-RAY DIFFRACTIONr_chiral_restr0.0890.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211077
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5531.5886
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0821450
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9313566
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2524.5518
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.796→1.843 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 61 -
Rwork0.272 1151 -
obs--98.94 %
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)
11.94610.5744-1.09371.7046-1.50715.47420.0734-0.23170.06870.1549-0.0419-0.0644-0.08980.2774-0.03150.04330.0116-0.00640.0453-0.0230.0899-2.689219.393620.6939
23.4557-0.18871.00191.6256-0.15695.94770.0102-0.1749-0.1509-0.02240.12540.12270.5333-0.3865-0.13560.0892-0.0310.00370.03720.01380.0869-14.44716.927318.9458
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 96
2X-RAY DIFFRACTION1A1097 - 1098
3X-RAY DIFFRACTION2B7 - 95
4X-RAY DIFFRACTION2B1096 - 1097

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