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- PDB-1ej9: CRYSTAL STRUCTURE OF HUMAN TOPOISOMERASE I DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1ej9
TitleCRYSTAL STRUCTURE OF HUMAN TOPOISOMERASE I DNA COMPLEX
Components
  • DNA (5'-D(*C*AP*AP*AP*AP*AP*GP*AP*CP*TP*CP*AP*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3')
  • DNA (5'-D(*C*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*TP*GP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3')
  • DNA TOPOISOMERASE I
KeywordsISOMERASE/DNA / protein-dna complex / type I topoisomerase / human / ISOMERASE-DNA COMPLEX
Function / homology
Function and homology information


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 / phosphorylation / male germ cell nucleus ...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 / phosphorylation / male germ cell nucleus / protein-DNA complex / chromosome segregation / circadian regulation of gene expression / P-body / fibrillar center / circadian rhythm / single-stranded DNA binding / chromosome / double-stranded DNA binding / peptidyl-serine phosphorylation / perikaryon / DNA replication / chromatin remodeling / response to xenobiotic stimulus / 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
Topoisomerase I; Chain A, domain 4 - #10 / : / Yeast DNA topoisomerase - domain 1 / DNA Topoisomerase I; domain 2 / DNA Topoisomerase I, domain 2 / DNA topoisomerase I, DNA binding, eukaryotic-type / DNA topoisomerase I, DNA binding, N-terminal domain 2 / DNA topoisomerase I, DNA binding, N-terminal domain 1 / DNA topoisomerase I, eukaryotic-type / DNA topoisomerase I, catalytic core, alpha/beta subdomain ...Topoisomerase I; Chain A, domain 4 - #10 / : / Yeast DNA topoisomerase - domain 1 / DNA Topoisomerase I; domain 2 / DNA Topoisomerase I, domain 2 / DNA topoisomerase I, DNA binding, eukaryotic-type / DNA topoisomerase I, DNA binding, N-terminal domain 2 / DNA topoisomerase I, DNA binding, N-terminal domain 1 / DNA topoisomerase I, eukaryotic-type / DNA topoisomerase I, catalytic core, alpha/beta subdomain / Topoisomerase I C-terminal domain / DNA topoisomerase I, DNA binding, eukaryotic-type, N-terminal domain superfamily / : / Eukaryotic DNA topoisomerase I, DNA binding fragment / C-terminal topoisomerase domain / DNA Topoisomerase I (eukaryota) / Topoisomerase (Topo) IB-type catalytic domain profile. / Topoisomerase I; Chain A, domain 3 / Topoisomerase I; Chain A, domain 3 / DNA topoisomerase I, active site / Topoisomerase (Topo) IB-type active site signature. / DNA topoisomerase I / DNA topoisomerase I, catalytic core, eukaryotic-type / DNA topoisomerase I, catalytic core, alpha-helical subdomain, eukaryotic-type / Eukaryotic DNA topoisomerase I, catalytic core / DNA breaking-rejoining enzyme, catalytic core / Topoisomerase I; Chain A, domain 4 / Beta Complex / Arc Repressor Mutant, subunit A / Alpha-Beta Complex / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA topoisomerase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsRedinbo, M.R. / Champoux, J.J. / Hol, W.G.
CitationJournal: Biochemistry / Year: 2000
Title: Novel insights into catalytic mechanism from a crystal structure of human topoisomerase I in complex with DNA.
Authors: Redinbo, M.R. / Champoux, J.J. / Hol, W.G.
History
DepositionMar 1, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: DNA (5'-D(*C*AP*AP*AP*AP*AP*GP*AP*CP*TP*CP*AP*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3')
D: DNA (5'-D(*C*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*TP*GP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3')
A: DNA TOPOISOMERASE I


Theoretical massNumber of molelcules
Total (without water)80,6693
Polymers80,6693
Non-polymers00
Water6,359353
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.98, 124.92, 72.29
Angle α, β, γ (deg.)90.0, 93.84, 90.0
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: DNA chain DNA (5'-D(*C*AP*AP*AP*AP*AP*GP*AP*CP*TP*CP*AP*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3')


Mass: 7064.639 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*C*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*TP*GP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3')


Mass: 7010.554 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein DNA TOPOISOMERASE I / E.C.5.99.1.2


Mass: 66593.836 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, RESIDUES 203-765 / Mutation: Y723F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): SF9 INSECT CELLS / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11387, EC: 5.99.1.2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.12 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 27% PEG 400, 145 mM MgCl2, 20 mM MES pH 6.8, 5 mM Tris pH 8.0, 30 mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1MES11
2Tris11
3DTT11
4PEG 40011
5MgCl211
6PEG 40012
7MgCl212
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
210 mMTris-HCl1drop
31 mMEDTA1drop
45 mMdithiothreitol1drop
55 mMTris-HCl1reservoir
620 mMMes-NaOH1reservoir
727 %PEG4001reservoir
8145 mM1reservoirMgCl2
930 mMdithiothreitol1reservoir
100.1 mMoligonucleotide1reservoir
116 mM1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1
DetectorType: OTHER / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→15 Å / Num. all: 105936 / Num. obs: 29834 / % possible obs: 0.968 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Biso Wilson estimate: 56.2 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 21.1
Reflection shellHighest resolution: 2.6 Å / Redundancy: 3 % / Rmerge(I) obs: 0.288 / % possible all: 0.87

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.6→15 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.281 2139 7 %random
Rwork0.214 ---
all-29834 --
obs-29616 98.68 %-
Refinement stepCycle: LAST / Resolution: 2.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3966 896 0 353 5215
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_angle_deg1.74
X-RAY DIFFRACTIONx_torsion_deg22.1
X-RAY DIFFRACTIONx_torsion_impr_deg1.58
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.58
LS refinement shell
*PLUS
Rfactor Rfree: 0.366 / Rfactor Rwork: 0.32

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