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- PDB-4fm9: Human topoisomerase II alpha bound to DNA -

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Basic information

Entry
Database: PDB / ID: 4fm9
TitleHuman topoisomerase II alpha bound to DNA
Components
  • DNA (5'-D(*CP*GP*CP*GP*CP*AP*TP*CP*GP*TP*CP*AP*TP*CP*CP*TP*C)-3')
  • DNA (5'-D(P*GP*AP*GP*GP*AP*TP*GP*AP*CP*GP*AP*TP*G)-3')
  • DNA topoisomerase 2-alpha
KeywordsISOMERASE/DNA / TOPOISOMERASE / DNA-BINDING / PROTEIN-DNA COMPLEX / ISOMERASE-DNA COMPLEX
Function / homology
Function and homology information


negative regulation of DNA duplex unwinding / positive regulation of single stranded viral RNA replication via double stranded DNA intermediate / sister chromatid segregation / apoptotic chromosome condensation / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / resolution of meiotic recombination intermediates / female meiotic nuclear division / embryonic cleavage / DNA ligation / Transcription of E2F targets under negative control by DREAM complex ...negative regulation of DNA duplex unwinding / positive regulation of single stranded viral RNA replication via double stranded DNA intermediate / sister chromatid segregation / apoptotic chromosome condensation / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / resolution of meiotic recombination intermediates / female meiotic nuclear division / embryonic cleavage / DNA ligation / Transcription of E2F targets under negative control by DREAM complex / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA binding, bending / DNA topological change / SUMOylation of DNA replication proteins / chromosome, centromeric region / ATP-dependent activity, acting on DNA / hematopoietic progenitor cell differentiation / condensed chromosome / protein kinase C binding / ubiquitin binding / male germ cell nucleus / chromosome segregation / regulation of circadian rhythm / rhythmic process / ribonucleoprotein complex / positive regulation of apoptotic process / protein heterodimerization activity / DNA damage response / chromatin binding / nucleolus / magnesium ion binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
Dna Ligase; domain 1 - #30 / Topoisomerase II; domain 5 / Topoisomerase II, domain 5 / DTHCT / DTHCT (NUC029) region / Topoisomerase, domain 3 / Topoisomerase; domain 3 / DNA topoisomerase 2, TOPRIM domain / Rossmann fold - #670 / Gyrase A; domain 2 - #40 ...Dna Ligase; domain 1 - #30 / Topoisomerase II; domain 5 / Topoisomerase II, domain 5 / DTHCT / DTHCT (NUC029) region / Topoisomerase, domain 3 / Topoisomerase; domain 3 / DNA topoisomerase 2, TOPRIM domain / Rossmann fold - #670 / Gyrase A; domain 2 - #40 / DNA topoisomerase II, eukaryotic-type / C-terminal associated domain of TOPRIM / C-terminal associated domain of TOPRIM / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / Toprim domain / DNA topoisomerase, type IIA-like domain superfamily / Toprim domain profile. / TOPRIM domain / Gyrase A; domain 2 / Dna Ligase; domain 1 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Complex / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA topoisomerase 2-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.901 Å
AuthorsWendorff, T.J. / Schmidt, B.H. / Heslop, P. / Austin, C.A. / Berger, J.M.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: The Structure of DNA-Bound Human Topoisomerase II Alpha: Conformational Mechanisms for Coordinating Inter-Subunit Interactions with DNA Cleavage.
Authors: Wendorff, T.J. / Schmidt, B.H. / Heslop, P. / Austin, C.A. / Berger, J.M.
History
DepositionJun 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA topoisomerase 2-alpha
C: DNA (5'-D(P*GP*AP*GP*GP*AP*TP*GP*AP*CP*GP*AP*TP*G)-3')
D: DNA (5'-D(*CP*GP*CP*GP*CP*AP*TP*CP*GP*TP*CP*AP*TP*CP*CP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,4786
Polymers97,3383
Non-polymers1413
Water79344
1
A: DNA topoisomerase 2-alpha
C: DNA (5'-D(P*GP*AP*GP*GP*AP*TP*GP*AP*CP*GP*AP*TP*G)-3')
D: DNA (5'-D(*CP*GP*CP*GP*CP*AP*TP*CP*GP*TP*CP*AP*TP*CP*CP*TP*C)-3')
hetero molecules

A: DNA topoisomerase 2-alpha
C: DNA (5'-D(P*GP*AP*GP*GP*AP*TP*GP*AP*CP*GP*AP*TP*G)-3')
D: DNA (5'-D(*CP*GP*CP*GP*CP*AP*TP*CP*GP*TP*CP*AP*TP*CP*CP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,95712
Polymers194,6756
Non-polymers2816
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area16600 Å2
ΔGint-91 kcal/mol
Surface area73030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.918, 215.081, 128.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1323-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA topoisomerase 2-alpha / DNA topoisomerase II / alpha isozyme


Mass: 88157.641 Da / Num. of mol.: 1 / Fragment: residues 431-1193
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOP2, TOP2A / Plasmid: PGAL / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BCY123 / References: UniProt: P11388, EC: 5.99.1.3

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (5'-D(P*GP*AP*GP*GP*AP*TP*GP*AP*CP*GP*AP*TP*G)-3')


Mass: 4080.671 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*GP*CP*GP*CP*AP*TP*CP*GP*TP*CP*AP*TP*CP*CP*TP*C)-3')


Mass: 5099.298 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 47 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 3.05 Å3/Da / Density % sol: 59.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG 3000, 100mM Na-cacodylate, 200mM MgCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 28, 2011
RadiationMonochromator: DOUBLE FLAT CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 2.9→80 Å / Num. all: 26736 / Num. obs: 25479 / % possible obs: 95.3 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.093 / Χ2: 1.141 / Net I/σ(I): 11.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.9-34.50.71223951.291191.6
3-3.124.50.44424271.268191.4
3.12-3.274.50.28824121.248191.9
3.27-3.447.70.38725591.528196.7
3.44-3.658.40.26926051.34198.5
3.65-3.948.40.18226191.219198.3
3.94-4.338.40.12425980.988197.8
4.33-4.968.50.08626080.932197.3
4.96-6.258.40.08326070.973196.1
6.25-808.20.04426490.881193.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 51.08 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.91 Å41.36 Å
Translation2.91 Å41.36 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.901→49.611 Å / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.698 / SU ML: 0.48 / σ(F): 1.34 / Phase error: 34.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2702 1285 5.06 %RANDOM
Rwork0.2269 ---
all0.2291 26736 --
obs0.2291 25373 94.68 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.262 Å2 / ksol: 0.317 e/Å3
Displacement parametersBiso max: 212.36 Å2 / Biso mean: 79.8838 Å2 / Biso min: 15.22 Å2
Baniso -1Baniso -2Baniso -3
1-99.6153 Å20 Å20 Å2
2--19.9227 Å20 Å2
3---17.8605 Å2
Refinement stepCycle: LAST / Resolution: 2.901→49.611 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5918 612 8 44 6582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066729
X-RAY DIFFRACTIONf_angle_d0.8479197
X-RAY DIFFRACTIONf_chiral_restr0.0471008
X-RAY DIFFRACTIONf_plane_restr0.0041070
X-RAY DIFFRACTIONf_dihedral_angle_d15.5482621
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9015-3.01760.47351250.44592443256888
3.0176-3.15490.46421360.35692569270591
3.1549-3.32120.37641360.30482567270392
3.3212-3.52930.34391440.28032737288198
3.5293-3.80170.32761470.25962725287298
3.8017-4.18410.24071550.21862747290298
4.1841-4.78910.22581720.17542734290697
4.7891-6.03210.23361520.20492747289996
6.0321-49.61850.23061180.19962819293794
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0143-0.02410.00180.0157-0.0140.0223-0.00840.0431-0.2617-0.0398-0.045-0.06110.0903-0.044-01.0240.0708-0.02320.3897-0.13890.521335.539913.64816.0464
2-0.00270.00110.00210.06490.04360.01810.0919-0.08560.0133-0.01560.0521-0.0987-0.02920.10070.08120.2430.0116-0.21040.4078-0.13110.32337.652126.838723.4072
30.0612-0.0039-0.03950.03190.0230.0396-0.0632-0.2096-0.21470.08440.00840.00780.13350.0095-0.0799-0.17070.1067-0.22890.2119-0.00260.465518.009319.288733.2846
40.11560.01060.01340.0198-0.0230.06330.1180.02710.00640.01320.1490.2902-0.2977-0.12960.24350.11180.2343-0.33740.27620.01840.399815.000639.563124.473
50.15370.0638-0.05690.0693-0.04070.0607-0.1079-0.0629-0.0781-0.31940.10540.0294-0.16140.0656-0.0230.6649-0.1256-0.18680.01960.06140.222543.468347.213816.5875
60.17660.07480.1170.1183-0.04450.152-0.19480.12660.0416-0.66290.1693-0.004-0.46520.0088-0.05780.8195-0.13150.11760.2829-0.04290.171648.543634.18660.6475
70.0384-0.02590.030.0437-0.05540.0367-0.0762-0.1090.1654-0.16360.0443-0.0362-0.0267-0.04920.02241.24750.0432-0.58730.19080.10810.486236.735888.635510.7557
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN C AND RESID 1:9 ) OR ( CHAIN D AND RESID 9:17 )C1 - 9
2X-RAY DIFFRACTION1( CHAIN C AND RESID 1:9 ) OR ( CHAIN D AND RESID 9:17 )D9 - 17
3X-RAY DIFFRACTION2( CHAIN C AND RESID 10:13 ) OR ( CHAIN D AND RESID 1:8 )C10 - 13
4X-RAY DIFFRACTION2( CHAIN C AND RESID 10:13 ) OR ( CHAIN D AND RESID 1:8 )D1 - 8
5X-RAY DIFFRACTION3( CHAIN A AND RESID 433:576 )A433 - 576
6X-RAY DIFFRACTION4( CHAIN A AND RESID 577:716 )A577 - 716
7X-RAY DIFFRACTION5( CHAIN A AND RESID 717:847 )A717 - 847
8X-RAY DIFFRACTION6( CHAIN A AND ( RESID 848:1044 OR RESID 1163:1190 ) )A848 - 1044
9X-RAY DIFFRACTION6( CHAIN A AND ( RESID 848:1044 OR RESID 1163:1190 ) )A1163 - 1190
10X-RAY DIFFRACTION7( CHAIN A AND RESID 1045:1162 )A1045 - 1162

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