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- PDB-1a35: HUMAN TOPOISOMERASE I/DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1a35
TitleHUMAN TOPOISOMERASE I/DNA COMPLEX
Components
  • DNA (5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*TP*AP*GP*AP*AP*AP*AP*AP*(BRU)P*(BRU)P*TP*TP*T)-3')
  • DNA (5'-D(*AP*AP*AP*AP*AP*TP*+UP*+UP*+UP*+UP*CP*+UP*AP*AP*GP*TP*CP*TP*TP*TP*+ UP*T)-3')
  • PROTEIN (DNA TOPOISOMERASE I)
KeywordsISOMERASE/DNA / TOPOISOMERASE I/DNA) / DNA / TOPOISOMERASE I / ISOMERASE-DNA COMPLEX
Function / homology
Function and homology information


DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / programmed cell death / embryonic cleavage / supercoiled DNA binding / DNA binding, bending / SUMOylation of DNA replication proteins / DNA topological change / male germ cell nucleus / chromosome segregation ...DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / programmed cell death / embryonic cleavage / supercoiled DNA binding / DNA binding, bending / SUMOylation of DNA replication proteins / DNA topological change / male germ cell nucleus / chromosome segregation / P-body / protein-DNA complex / circadian regulation of gene expression / fibrillar center / circadian rhythm / single-stranded DNA binding / chromosome / perikaryon / double-stranded DNA binding / peptidyl-serine phosphorylation / DNA replication / chromatin remodeling / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / phosphorylation / 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 / RIGID BODY REFINEMENT / Resolution: 2.5 Å
AuthorsRedinbo, M.R. / Stewart, L. / Kuhn, P. / Champoux, J.J. / Hol, W.G.
CitationJournal: Science / Year: 1998
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
DepositionJan 29, 1998Deposition site: BNL / Processing site: NDB
Revision 1.0Aug 28, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)84,0383
Polymers84,0383
Non-polymers00
Water4,918273
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.800, 66.300, 71.800
Angle α, β, γ (deg.)90.00, 98.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 6920.208 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*AP*AP*AP*AP*AP*TP*+UP*+UP*+UP*+UP*CP*+UP*AP*AP*GP*TP*CP*TP*TP*TP*+ UP*T)-3')


Mass: 7094.593 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (DNA TOPOISOMERASE I) / E.C.5.99.1.2


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.) Homo sapiens (human) / Cellular location: NUCLEUSCell nucleus / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11387, DNA topoisomerase
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRESIDUES 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 RECONSTITUTED ENZYME. THE RECONSTITUTED ENZYME IS MADE UP OF RESIDUES 175-659 OF THE CORE (EXPRESSED IN BACULOVIRUS) AND RESIDUES 713-765 OF THE C-TERMINAL DOMAIN (EXPRESSED IN E. COLI). CHAIN A RESIDUES 175-214 AND 636-659 OF THE CORE AND 713-719 OF THE C-TERMINAL DOMAIN ARE DISORDERED AND NOT PRESENT IN THE STRUCTURE. TER ALA 635 A IS THE TERMINAL RESIDUE OF THE CORE DOMAIN. PHE 765 A IS THE TERMINAL RESIDUE OF THE C-TERMINAL DOMAIN. THY 22 C IS THE 3' TERMINAL NUCLEOTIDE OF THE SCISSILE STRAND OF THE DNA DUPLEX. THY 122 D IS THE 3' TERMINAL NUCLEOTIDE OF THE INTACT STRAND OF THE DNA DUPLEX.

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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: 2.01 Å3/Da / Density % sol: 38.91 %
Crystal growTemperature: 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
IDNameCrystal-IDSol-ID
1TRIS-HCLTris11
2EDTAEthylenediaminetetraacetic acid11
3DTT11
4MGCL211
5PEG 40011
6TRIS-HCLTris12
7MGCL212
8DTT12
9PEG 40012
10TRIS-HCLTris13
11MGCL213
12PEG 40013
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
18 %PEG4001reservoir
233.3 mM1reservoirMgCl2
335.5 mMTris1reservoirpH7.7
44.4 mMdithiothreitol1reservoir
60.01 mMoligo1drop
70.7 mM1dropNaCl
81 mg/mlprotein1drop
90.2 mMEDTA1drop
5water1drop0.003ml
102 mMTris-HCl1droppH7.5
112 mMdithiothreitol1drop
121

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jun 1, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.308 1467 7 %RANDOM
Rwork0.209 ---
obs-20807 87 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.35 Å20 Å20.753 Å2
2--4.706 Å20 Å2
3----2.35 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3778 888 8 273 4947
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.47
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.46
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.5→2.59 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.321 81 6 %
Rwork0.315 1261 -
obs--55.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM_NDBX.DNATOP_NDBX.DNA
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
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
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.46
LS refinement shell
*PLUS
% reflection Rfree: 6 %

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