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- PDB-1k4s: HUMAN DNA TOPOISOMERASE I IN COVALENT COMPLEX WITH A 22 BASE PAIR... -

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Basic information

Entry
Database: PDB / ID: 1k4s
TitleHUMAN DNA TOPOISOMERASE I IN COVALENT COMPLEX WITH A 22 BASE PAIR DNA DUPLEX
Components
  • 5'-D(*(SPT)P*GP*AP*AP*AP*AP*AP*(5IU)P*(5IU)P*(5IU)P*(5IU)P*T)-3'
  • 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*(5IU)P*(5IU))-3'
  • 5'-D(*AP*AP*AP*AP*AP*TP*(IDO)UP*(IDO)UP*(IDO)UP*(IDO)UP*CP*AP*AP*AP*GP*(IDO)UP*CP*(IDO)UP*(IDO)UP*(IDO)UP*(IDO)UP*T)-3'
  • DNA topoisomerase ITopoisomerase
KeywordsISOMERASE/DNA / Complex (ISOMERASE-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 / protein-DNA complex / P-body / 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 / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsStaker, B.L. / Hjerrild, K. / Feese, M.D. / Behnke, C.A. / Burgin Jr., A.B. / Stewart, L.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: The mechanism of topoisomerase I poisoning by a camptothecin analog
Authors: Staker, B.L. / Hjerrild, K. / Feese, M.D. / Behnke, C.A. / Burgin Jr., A.B. / Stewart, L.J.
History
DepositionOct 8, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_comp_id / _struct_conn.ptnr1_auth_seq_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 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)85,3934
Polymers85,3934
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.235, 73.235, 186.632
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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*(5IU)P*(5IU))-3'


Mass: 3284.796 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*(SPT)P*GP*AP*AP*AP*AP*AP*(5IU)P*(5IU)P*(5IU)P*(5IU)P*T)-3'


Mass: 4138.985 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*AP*AP*AP*AP*AP*TP*(IDO)UP*(IDO)UP*(IDO)UP*(IDO)UP*CP*AP*AP*AP*GP*(IDO)UP*CP*(IDO)UP*(IDO)UP*(IDO)UP*(IDO)UP*T)-3'


Mass: 7721.218 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Protein DNA topoisomerase I / Topoisomerase


Mass: 70248.023 Da / Num. of mol.: 1
Fragment: Core Domain and C-Terminal Domain, Residues 174-765
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11387, DNA topoisomerase

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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: 3.43 Å3/Da / Density % sol: 64.17 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 8000, Tris-HCl, Na/K Phosphate, KCl, DTT, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2Tris-HClTris11
3Na/K Phosphate11
4KCl11
5DTT11
Crystal grow
*PLUS
Temperature: 16 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 %(w/v)PEG80001reservoir
2100 mM1reservoirpH8.0
3100 mMsodium potassium phosphate1reservoirpH6.2
4100 mM1reservoirKCl
510 mMdithiothreitol1reservoir
60.1 mMsuicide duplex substrate1drop
74 mg/mltopo701drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 18471 / Num. obs: 18471 / % possible obs: 85.9 % / Rsym value: 0.13
Reflection shellResolution: 3.2→3.31 Å / Mean I/σ(I) obs: 2.95 / Rsym value: 0.13 / % possible all: 69.5
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 17874 / Rmerge(I) obs: 0.13

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNXrefinement
CNXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A36

1a36


Resolution: 3.2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2223 1561 -Rfree reflections selected to maintain twin pairs in same set.
Rwork0.2166 ---
all-17874 --
obs-17874 96.8 %-
Displacement parametersBiso mean: 41.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3966 877 15 0 4858
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0088
X-RAY DIFFRACTIONc_angle_deg1.361
X-RAY DIFFRACTIONc_dihedral_angle_d22.158
X-RAY DIFFRACTIONc_improper_angle_d3.352
Refinement
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 50 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.284 / Rfactor Rwork: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.36
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.16
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg3.35

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