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- PDB-1nh3: Human Topoisomerase I Ara-C Complex -

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Basic information

Entry
Database: PDB / ID: 1nh3
TitleHuman Topoisomerase I Ara-C Complex
Components
  • 5'-D(*(GNG)P*GP*AP*AP*AP*AP*AP*UP*UP*UP*UP*T)-3'
  • 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*UP*(UBB))-3'
  • 5'-D(*AP*AP*AP*AP*AP*TP*UP*UP*UP*UP*CP*(CAR)P*AP*AP*GP*UP*CP*UP*UP*UP*UP*T)-3'
  • DNA topoisomerase I
KeywordsISOMERASE/DNA / Ara-C / protein-DNA complex / DNA damage / isomerase / 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/RNA hybrid / DNA/RNA hybrid (> 10) / DNA topoisomerase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsChrencik, J.E. / Burgin, A.B. / Pommier, Y. / Stewart, L. / Redinbo, M.R.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Structural Impact of the Leukemia Drug 1-beta-D-Arabinofuranosylcytosine (Ara-C) on the Covalent Human Topoisomerase I-DNA Complex
Authors: Chrencik, J.E. / Burgin, A.B. / Pommier, Y. / Stewart, L. / Redinbo, M.R.
History
DepositionDec 18, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE The DNA (duplex oligo) was added to the protein during crystallization. At this time, the ...SEQUENCE The DNA (duplex oligo) was added to the protein during crystallization. At this time, the protein initiates a transesterification reaction in which one strand of DNA is broken into chains B and C, and the protein chain A is covalently linked to the DNA through residue 723.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*UP*(UBB))-3'
C: 5'-D(*(GNG)P*GP*AP*AP*AP*AP*AP*UP*UP*UP*UP*T)-3'
D: 5'-D(*AP*AP*AP*AP*AP*TP*UP*UP*UP*UP*CP*(CAR)P*AP*AP*GP*UP*CP*UP*UP*UP*UP*T)-3'
A: DNA topoisomerase I


Theoretical massNumber of molelcules
Total (without water)79,8954
Polymers79,8954
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.97, 72.97, 186.29
Angle α, β, γ (deg.)90, 90, 120
Int Tables number145
Space group name H-MP32

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Components

#1: DNA chain 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*UP*(UBB))-3'


Mass: 3017.004 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*(GNG)P*GP*AP*AP*AP*AP*AP*UP*UP*UP*UP*T)-3'


Mass: 3564.368 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA/RNA hybrid 5'-D(*AP*AP*AP*AP*AP*TP*UP*UP*UP*UP*CP*(CAR)P*AP*AP*GP*UP*CP*UP*UP*UP*UP*T)-3'


Mass: 6580.128 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Protein DNA topoisomerase I


Mass: 66733.867 Da / Num. of mol.: 1 / Fragment: Core Subdomain, C-Terminal Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOP1 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11387, EC: 5.99.1.2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.56 Å3/Da / Density % sol: 65.41 %
Crystal growTemperature: 276 K / Method: vapor diffusion, sitting drop / pH: 7.7
Details: Tris, Magnesium Chloride, PEG 400, DTT, pH 7.7, VAPOR DIFFUSION, SITTING DROP, temperature 276K
Crystal grow
*PLUS
Temperature: 22 ℃ / Details: Redinbo, M.R., (1998) Science, 279, 1504.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
18 %PEG4001drop
233.3 mM1dropMgCl2
335.5 mMTris1drop
44.4 mMdithiothreitol1drop
60.01 mMoligo1drop
70.7 mM1dropNaCl
81 mg/mlprotein1drop
90.2 mMEDTA1drop
5water1drop0.003ml

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 18, 2001
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 13878 / Num. obs: 13878 / % possible obs: 69.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.1→3.21 Å / % possible all: 54.7
Reflection
*PLUS
Lowest resolution: 100 Å / Redundancy: 12.2 % / Num. measured all: 169504 / Rmerge(I) obs: 0.135
Reflection shell
*PLUS
Lowest resolution: 3.2 Å / % possible obs: 54.7 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 1.4

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1A31

1a31


Resolution: 3.1→44.29 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.311 1351 -random
Rwork0.235 ---
all0.235 ---
obs0.235 13878 74.6 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-27.26 Å213.437 Å20 Å2
2--27.26 Å20 Å2
3----54.52 Å2
Refine analyzeLuzzati coordinate error obs: 0.48 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.71 Å
Refinement stepCycle: LAST / Resolution: 3.1→44.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3483 878 0 33 4394
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.026
X-RAY DIFFRACTIONc_angle_d1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d3.88
Refinement
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 100 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.243 / Rfactor Rwork: 0.309
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0118
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.55
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.59

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