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Open data
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Basic information
Entry | Database: PDB / ID: 4ayc | ||||||
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Title | RNF8 RING domain structure | ||||||
![]() | (E3 UBIQUITIN-PROTEIN LIGASE ...) x 2 | ||||||
![]() | LIGASE / DNA DAMAGE / K63 CHAINS | ||||||
Function / homology | ![]() sperm DNA condensation / protein K6-linked ubiquitination / isotype switching / DNA repair-dependent chromatin remodeling / response to ionizing radiation / cell division site / negative regulation of transcription elongation by RNA polymerase II / protein K63-linked ubiquitination / positive regulation of double-strand break repair via homologous recombination / signal transduction in response to DNA damage ...sperm DNA condensation / protein K6-linked ubiquitination / isotype switching / DNA repair-dependent chromatin remodeling / response to ionizing radiation / cell division site / negative regulation of transcription elongation by RNA polymerase II / protein K63-linked ubiquitination / positive regulation of double-strand break repair via homologous recombination / signal transduction in response to DNA damage / protein autoubiquitination / protein K48-linked ubiquitination / interstrand cross-link repair / epigenetic regulation of gene expression / ubiquitin ligase complex / positive regulation of DNA repair / ubiquitin binding / Nonhomologous End-Joining (NHEJ) / RING-type E3 ubiquitin transferase / G2/M DNA damage checkpoint / double-strand break repair via nonhomologous end joining / ubiquitin protein ligase activity / double-strand break repair / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / Processing of DNA double-strand break ends / midbody / histone binding / ubiquitin-dependent protein catabolic process / chromosome, telomeric region / cell cycle / cell division / ubiquitin protein ligase binding / DNA damage response / chromatin binding / protein homodimerization activity / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mattiroli, F. / Vissers, J.H.A. / Van Dijk, W.J. / Ikpa, P. / Citterio, E. / Vermeulen, W. / Marteijn, J.A. / Sixma, T.K. | ||||||
![]() | ![]() Title: Rnf168 Ubiquitinates K13-15 on H2A/H2Ax to Drive DNA Damage Signaling Authors: Mattiroli, F. / Vissers, J.H.A. / Van Dijk, W.J. / Ikpa, P. / Citterio, E. / Vermeulen, W. / Marteijn, J.A. / Sixma, T.K. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 129.2 KB | Display | ![]() |
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PDB format | ![]() | 101.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 752.1 KB | Display | ![]() |
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Full document | ![]() | 754.4 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 17.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-E3 UBIQUITIN-PROTEIN LIGASE ... , 2 types, 2 molecules AB
#1: Protein | Mass: 16353.082 Da / Num. of mol.: 1 / Fragment: RING DOMAIN, RESIDUES 351-485 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O76064, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
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#2: Protein | Mass: 16369.082 Da / Num. of mol.: 1 / Fragment: RING DOMAIN, RESIDUES 351-485 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O76064, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
-Non-polymers , 6 types, 68 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/CPQ.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CPQ.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-CPQ / | #5: Chemical | ChemComp-ZN / #6: Chemical | ChemComp-GOL / | #7: Chemical | ChemComp-CL / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.1 % / Description: NONE |
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Crystal grow | pH: 6.9 Details: 0.1 M NA CACODYLATE, PH 6.9, 2.5 M AMMONIUM SULPHATE, 0.8 MM N,N-BIS(3-D-GLUCONAMIDOPROPYL)DEOXYCHOLAMIDE |
-Data collection
Diffraction | Mean temperature: 193 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2010 |
Radiation | Monochromator: FIXED-EXIT LN2 COOLED DOUBLE CRYSTAL MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.282 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→47.37 Å / Num. obs: 28115 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 25.8 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.7 / % possible all: 95.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 1.9→46.29 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.953 / SU B: 7.513 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: RELATIVE TO THE PUBLICATION TWO SIDECHAIN WERE ADDED TO THE MODEL (RESIDUES A482 AND B485) RESULTING IN SLIGHTLY DIFFERENT STATISTICS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.632 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→46.29 Å
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