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Yorodumi- PDB-3g65: Crystal Structure of the Human Rad9-Rad1-Hus1 DNA Damage Checkpoi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3g65 | ||||||
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Title | Crystal Structure of the Human Rad9-Rad1-Hus1 DNA Damage Checkpoint Complex | ||||||
Components |
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Keywords | CELL CYCLE / PCNA / DNA BINDING CLAMP / DNA damage / DNA repair / Exonuclease / Hydrolase / Nuclease / Nucleus / Phosphoprotein | ||||||
Function / homology | Function and homology information meiotic DNA integrity checkpoint signaling / checkpoint clamp complex / meiotic recombination checkpoint signaling / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / DNA replication checkpoint signaling / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / mitotic DNA replication checkpoint signaling / mitotic intra-S DNA damage checkpoint signaling / embryo development ending in birth or egg hatching ...meiotic DNA integrity checkpoint signaling / checkpoint clamp complex / meiotic recombination checkpoint signaling / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / DNA replication checkpoint signaling / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / mitotic DNA replication checkpoint signaling / mitotic intra-S DNA damage checkpoint signaling / embryo development ending in birth or egg hatching / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / Presynaptic phase of homologous DNA pairing and strand exchange / Activation of ATR in response to replication stress / response to UV / substantia nigra development / 3'-5' exonuclease activity / telomere maintenance / DNA damage checkpoint signaling / cellular response to ionizing radiation / nucleotide-excision repair / regulation of protein phosphorylation / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / histone deacetylase binding / SH3 domain binding / intrinsic apoptotic signaling pathway in response to DNA damage / chromosome / site of double-strand break / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / intracellular membrane-bounded organelle / DNA repair / DNA damage response / nucleolus / protein kinase binding / enzyme binding / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Dore, A.S. / Kilkenny, M.L. / Rzechorzek, N.J. / Pearl, L.H. | ||||||
Citation | Journal: Mol.Cell / Year: 2009 Title: Crystal structure of the rad9-rad1-hus1 DNA damage checkpoint complex--implications for clamp loading and regulation. Authors: Dore, A.S. / Kilkenny, M.L. / Rzechorzek, N.J. / Pearl, L.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g65.cif.gz | 322.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g65.ent.gz | 263.1 KB | Display | PDB format |
PDBx/mmJSON format | 3g65.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3g65_validation.pdf.gz | 455.2 KB | Display | wwPDB validaton report |
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Full document | 3g65_full_validation.pdf.gz | 471.4 KB | Display | |
Data in XML | 3g65_validation.xml.gz | 30.4 KB | Display | |
Data in CIF | 3g65_validation.cif.gz | 40.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g6/3g65 ftp://data.pdbj.org/pub/pdb/validation_reports/g6/3g65 | HTTPS FTP |
-Related structure data
Related structure data | 1axcS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32452.266 Da / Num. of mol.: 1 / Fragment: UNP residues 1-270 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAD9, RAD9A / Plasmid: pFBDM / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: Q99638, exodeoxyribonuclease III |
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#2: Protein | Mass: 31854.201 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAD1, REC1 / Plasmid: pFBDM / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: O60671, exodeoxyribonuclease III |
#3: Protein | Mass: 31731.854 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HUS1 / Plasmid: pFBDM / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: O60921 |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M Tris-HCl, 17% PEG 2000-Mme, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.9→82 Å / Num. all: 19109 / Num. obs: 18454 / % possible obs: 97.6 % / Redundancy: 4.5 % / Biso Wilson estimate: 76.6 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.115 / Net I/σ(I): 3.1 | |||||||||||||||
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2593 / Rsym value: 0.326 / % possible all: 94 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AXC Resolution: 2.9→82 Å / SU ML: 0.4 / σ(F): 1.38 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.893 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→82 Å
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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