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Open data
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Basic information
Entry | Database: PDB / ID: 1a35 | ||||||
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Title | HUMAN TOPOISOMERASE I/DNA COMPLEX | ||||||
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![]() | ISOMERASE/DNA / TOPOISOMERASE I/DNA) / DNA / TOPOISOMERASE I / ISOMERASE-DNA COMPLEX | ||||||
Function / homology | ![]() DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / embryonic cleavage / programmed cell death / supercoiled DNA binding / DNA binding, bending / DNA topological change / SUMOylation of DNA replication proteins / male germ cell nucleus / chromosome segregation ...DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / embryonic cleavage / programmed cell death / supercoiled DNA binding / DNA binding, bending / DNA topological change / SUMOylation of DNA replication proteins / male germ cell nucleus / chromosome segregation / protein-DNA complex / circadian regulation of gene expression / P-body / fibrillar center / circadian rhythm / chromosome / single-stranded DNA binding / double-stranded DNA binding / peptidyl-serine phosphorylation / perikaryon / DNA replication / chromatin remodeling / response to xenobiotic stimulus / phosphorylation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / protein serine/threonine kinase activity / chromatin binding / nucleolus / DNA binding / RNA binding / nucleoplasm / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Redinbo, M.R. / Stewart, L. / Kuhn, P. / Champoux, J.J. / Hol, W.G. | ||||||
![]() | ![]() Title: Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA. Authors: Redinbo, M.R. / Stewart, L. / Kuhn, P. / Champoux, J.J. / Hol, W.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 144.2 KB | Display | ![]() |
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PDB format | ![]() | 105.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 394.5 KB | Display | ![]() |
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Full document | ![]() | 417.1 KB | Display | |
Data in XML | ![]() | 14.8 KB | Display | |
Data in CIF | ![]() | 23.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: DNA chain | Mass: 6920.208 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 7094.593 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 70022.859 Da / Num. of mol.: 1 / Fragment: CORE DOMAIN AND C-TERMINAL DOMAIN / Mutation: Y723F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Water | ChemComp-HOH / |
Compound details | RESIDUES 215-635 OF CHAIN A COMPRISE THE CORE DOMAIN OF THE MOLECULE. RESIDUES 715-765 OF CHAIN A ...RESIDUES 215-635 OF CHAIN A COMPRISE THE CORE DOMAIN OF THE MOLECULE. RESIDUES 715-765 OF CHAIN A COMPRISE THE C-TERMINAL DOMAIN. 1-22 OF CHAIN C COMPRISE THE SCISSILE STRAND OF THE DNA, 101-122 OF CHAIN D THE INTACT DNA STRAND. NOTE THAT THE LINKER DOMAIN (636-714) IS NOT PRESENT IN THE CONSTRUCT OF THIS RECONSTITU |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.91 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.7 Details: pH 7.70, VAPOR DIFFUSION, SITTING DROP, temperature 295.00K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 22 ℃ / pH: 7.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Jun 1, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 18834 / % possible obs: 83.9 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.077 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.269 / % possible all: 87.7 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 20 Å / % possible obs: 83.9 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Num. measured all: 78779 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 2.6 Å / % possible obs: 87.7 % / Redundancy: 4.2 % |
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Processing
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Refinement | Method to determine structure: RIGID BODY REFINEMENT Starting model: RECONSTITUTED HUMAN TOPOISOMERASE I COVALENT COMPLEX WITH 22 BASE PAIR DUPLEX DNA Resolution: 2.5→20 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 7 % / Rfactor obs: 0.209 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS % reflection Rfree: 6 % |