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- PDB-1seu: Human DNA Topoisomerase I (70 Kda) In Complex With The Indolocarb... -

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Basic information

Entry
Database: PDB / ID: 1seu
TitleHuman DNA Topoisomerase I (70 Kda) In Complex With The Indolocarbazole SA315F and Covalent Complex With A 22 Base Pair DNA Duplex
Components
  • 5'-D(*(TGP)P*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3'
  • 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T)-3'
  • 5'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*CP*AP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3'
  • DNA topoisomerase I
KeywordsISOMERASE/DNA / COMPLEX (ISOMERASE-DNA) / DNA / TOPOISOMERASE I / DRUG / POISON / 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 / protein-DNA complex ...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 / protein-DNA complex / male germ cell nucleus / 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
Chem-SA3 / DNA / DNA (> 10) / DNA topoisomerase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsStaker, B.L. / Feese, M.D. / Cushman, M. / Pommier, Y. / Zembower, D. / Stewart, L. / Burgin, A.B.
CitationJournal: J.Med.Chem. / Year: 2005
Title: Structures of three classes of anticancer agents bound to the human topoisomerase I-DNA covalent complex
Authors: Staker, B.L. / Feese, M.D. / Cushman, M. / Pommier, Y. / Zembower, D. / Stewart, L. / Burgin, A.B.
History
DepositionFeb 18, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 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 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 600HETEROGEN Atom O3* of thymine 10, chain B is missing due to the covalent bond formed between ...HETEROGEN Atom O3* of thymine 10, chain B is missing due to the covalent bond formed between thymine 10 and phosphotyrosine (PTR) 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*TP*T)-3'
C: 5'-D(*(TGP)P*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3'
D: 5'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*CP*AP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3'
A: DNA topoisomerase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,2085
Polymers83,6894
Non-polymers5191
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.382, 115.965, 73.547
Angle α, β, γ (deg.)90.00, 93.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 3061.057 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*(TGP)P*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3'


Mass: 3716.518 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*CP*AP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3'


Mass: 6690.362 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Protein DNA topoisomerase I


Mass: 70221.000 Da / Num. of mol.: 1 / Mutation: Asn722Ser
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOP1 / Plasmid: PFACTBAC1 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11387, EC: 5.99.1.2
#5: Chemical ChemComp-SA3 / 2,10-DIHYDROXY-12-(BETA-D-GLUCOPYRANOSYL)-6,7,12,13-TETRAHYDROINDOLO[2,3-A]PYRROLO[3,4-C]CARBAZOLE-5,7-DIONE


Mass: 519.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H21N3O9
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: 2.92 Å3/Da / Density % sol: 57.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: PEG 8000, AMMONIUM SULFATE, MES, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2AMMONIUM SULFATE11
3MES11
4AMMONIUM SULFATE12
5MES12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1.1 Å
DetectorDetector: CCD / Date: Jul 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 15533 / % possible obs: 80.5 % / Observed criterion σ(I): 0 / Rsym value: 0.107 / Net I/σ(I): 15.4
Reflection shellResolution: 3→3.16 Å / Mean I/σ(I) obs: 2.5 / Num. unique all: 973 / Rsym value: 0.325 / % possible all: 38.1

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Processing

Software
NameVersionClassification
CNX2002refinement
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K4T

1k4t


Resolution: 3→46.63 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1701025.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.295 1575 10.2 %RANDOM
Rwork0.237 ---
obs-15516 80.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.243353 e/Å3
Displacement parametersBiso mean: 78.3 Å2
Baniso -1Baniso -2Baniso -3
1--19.35 Å20 Å29.8 Å2
2---28.08 Å20 Å2
3---47.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 3→46.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4685 892 38 0 5615
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d3.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.821.5
X-RAY DIFFRACTIONc_mcangle_it3.172
X-RAY DIFFRACTIONc_scbond_it2.262
X-RAY DIFFRACTIONc_scangle_it3.682.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.393 112 9 %
Rwork0.357 1127 -
obs--38.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.PARAM
X-RAY DIFFRACTION5SA3_PAR.PARSA3_TOP.TOP

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