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- PDB-4cgy: Crystal structure of the human topoisomerase III alpha-RMI1 complex -
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Open data
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Basic information
Entry | Database: PDB / ID: 4cgy | ||||||
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Title | Crystal structure of the human topoisomerase III alpha-RMI1 complex | ||||||
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![]() | DNA REPLICATION/ISOMERASE / DNA REPLICATION-ISOMERASE COMPLEX / DOUBLE HOLLIDAY JUNCTION DISSOLUTION / DECATENATION / MINIMAL DISSOLVASOME | ||||||
Function / homology | ![]() RecQ family helicase-topoisomerase III complex / reduction of food intake in response to dietary excess / 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 ...RecQ family helicase-topoisomerase III complex / reduction of food intake in response to dietary excess / 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 / Presynaptic phase of homologous DNA pairing and strand exchange / DNA topological change / 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 / DNA replication / Regulation of TP53 Activity through Phosphorylation / nuclear body / mitochondrial matrix / nucleotide binding / DNA binding / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bocquet, N. / Bunker, R.D. / Thoma, N.H. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 343.9 KB | Display | ![]() |
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PDB format | ![]() | 279.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.5 KB | Display | ![]() |
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Full document | ![]() | 430.5 KB | Display | |
Data in XML | ![]() | 28.5 KB | Display | |
Data in CIF | ![]() | 39.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4chtC ![]() 1eclS ![]() 3nbiS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 86584.641 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-753 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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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.) ![]() ![]() |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: 8-12% (W/V) PEG 2000, 100 MM TRIS-HCL PH 7.0, 200 MM MGCL2 |
-Data collection
Diffraction | Mean temperature: 10 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2010 / Details: DYNAMICALLY BENDABLE MIRROR |
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: 2.85→62.78 Å / Num. obs: 41328 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 100 % / Biso Wilson estimate: 93.75 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2.85→2.97 Å / Redundancy: 14.7 % / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 1ECL AND 3NBI Resolution: 2.85→65.49 Å / Cor.coef. Fo:Fc: 0.9298 / Cor.coef. Fo:Fc free: 0.9116 / SU R Cruickshank DPI: 0.374 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.376 / SU Rfree Blow DPI: 0.26 / SU Rfree Cruickshank DPI: 0.263
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Displacement parameters | Biso mean: 80.28 Å2
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Refine analyze | Luzzati coordinate error obs: 0.439 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→65.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.85→2.92 Å / Total num. of bins used: 20
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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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