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Yorodumi- PDB-4cht: Crystal structure of the human topoisomerase III alpha-RMI1 compl... -
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-Basic information
Entry | Database: PDB / ID: 4cht | ||||||
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Title | Crystal structure of the human topoisomerase III alpha-RMI1 complex with bound calcium ion | ||||||
Components |
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Keywords | CELL CYCLE / DOUBLE HOLLIDAY JUNCTION DISSOLUTION / DECATENATION / MINIMAL DISSOLVASOME | ||||||
Function / homology | Function and homology information reduction of food intake in response to dietary excess / RecQ family helicase-topoisomerase III complex / DNA topoisomerase activity / resolution of DNA recombination intermediates / chromosome separation / DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / resolution of meiotic recombination intermediates / mitochondrial DNA metabolic process / Impaired BRCA2 binding to PALB2 ...reduction of food intake in response to dietary excess / RecQ family helicase-topoisomerase III complex / DNA topoisomerase activity / resolution of DNA recombination intermediates / chromosome separation / DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / resolution of meiotic recombination intermediates / mitochondrial DNA metabolic process / Impaired BRCA2 binding to PALB2 / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / DNA topological change / Presynaptic phase of homologous DNA pairing and strand exchange / response to glucose / meiotic cell cycle / double-strand break repair via homologous recombination / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / multicellular organism growth / PML body / Meiotic recombination / glucose homeostasis / single-stranded DNA binding / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / DNA replication / nuclear body / mitochondrial matrix / nucleotide binding / DNA binding / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å | ||||||
Authors | Bocquet, N. / Bunker, R.D. / Thoma, N.H. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2014 Title: Structural and Mechanistic Insight Into Holliday-Junction Dissolution by Topoisomerase Iiialpha and Rmi1 Authors: Bocquet, N. / Bizard, A.H. / Abdulrahman, W. / Larsen, N.B. / Faty, M. / Cavadini, S. / Bunker, R.D. / Kowalczykowski, S.C. / Cejka, P. / Hickson, I.D. / Thoma, N.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cht.cif.gz | 347.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cht.ent.gz | 282.3 KB | Display | PDB format |
PDBx/mmJSON format | 4cht.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ch/4cht ftp://data.pdbj.org/pub/pdb/validation_reports/ch/4cht | HTTPS FTP |
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-Related structure data
Related structure data | 4cgySC S: Starting model for refinement C: citing same article (ref.) |
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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: 86641.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q13472, DNA topoisomerase |
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#2: Protein | Mass: 24644.457 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-219 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q9H9A7 |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.4 Å3/Da / Density % sol: 77 % / Description: NONE |
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Crystal grow | pH: 7 Details: 8% (W/V) PEG 5000 MME, 200 MM CALCIUM CITRATE, 100 MM TRIS/HCL PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→65.05 Å / Num. obs: 27765 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 89.41 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 3.25→3.45 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4CGY Resolution: 3.25→65.05 Å / Cor.coef. Fo:Fc: 0.9089 / Cor.coef. Fo:Fc free: 0.8827 / SU R Cruickshank DPI: 1.559 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 2.132 / SU Rfree Blow DPI: 0.354 / SU Rfree Cruickshank DPI: 0.357
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Displacement parameters | Biso mean: 80.98 Å2
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Refine analyze | Luzzati coordinate error obs: 0.686 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.25→65.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.25→3.37 Å / Total num. of bins used: 14
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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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