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- PDB-8w50: Crystal structure of DNA binding and cleavage core of human topoi... -

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Basic information

Entry
Database: PDB / ID: 8w50
TitleCrystal structure of DNA binding and cleavage core of human topoisomerase 2-alpha in a DNA binding-competent conformation
ComponentsDNA topoisomerase 2-alpha
KeywordsDNA BINDING PROTEIN / eukaryotic DNA topoisomerase G-segment DNA binding cleavage center assembly
Function / homology
Function and homology information


: / positive regulation of single stranded viral RNA replication via double stranded DNA intermediate / apoptotic chromosome condensation / sister chromatid segregation / resolution of meiotic recombination intermediates / female meiotic nuclear division / embryonic cleavage / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / : / Transcription of E2F targets under negative control by DREAM complex ...: / positive regulation of single stranded viral RNA replication via double stranded DNA intermediate / apoptotic chromosome condensation / sister chromatid segregation / resolution of meiotic recombination intermediates / female meiotic nuclear division / embryonic cleavage / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / : / Transcription of E2F targets under negative control by DREAM complex / DNA binding, bending / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / SUMOylation of DNA replication proteins / chromosome, centromeric region / hematopoietic progenitor cell differentiation / ATP-dependent activity, acting on DNA / condensed chromosome / ubiquitin binding / male germ cell nucleus / chromosome segregation / protein kinase C binding / regulation of circadian rhythm / rhythmic process / positive regulation of apoptotic process / ribonucleoprotein complex / 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
DTHCT / DTHCT (NUC029) region / DNA topoisomerase 2, TOPRIM domain / C-terminal associated domain of TOPRIM / C-terminal associated domain of TOPRIM / DNA topoisomerase II, eukaryotic-type / : / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A ...DTHCT / DTHCT (NUC029) region / DNA topoisomerase 2, TOPRIM domain / C-terminal associated domain of TOPRIM / C-terminal associated domain of TOPRIM / DNA topoisomerase II, eukaryotic-type / : / 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 / 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
Similarity search - Domain/homology
DNA topoisomerase 2-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsChan, N.L. / Liu, K.T. / Chen, S.F.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
National Science Council (NSC, Taiwan) Taiwan
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Structural insights into the assembly of type IIA topoisomerase DNA cleavage-religation center.
Authors: Liu, K.T. / Chen, S.F. / Chan, N.L.
History
DepositionAug 25, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA topoisomerase 2-alpha
B: DNA topoisomerase 2-alpha
C: DNA topoisomerase 2-alpha
D: DNA topoisomerase 2-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)371,9597
Polymers371,6714
Non-polymers2883
Water6,882382
1
A: DNA topoisomerase 2-alpha
B: DNA topoisomerase 2-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,1245
Polymers185,8362
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA topoisomerase 2-alpha
D: DNA topoisomerase 2-alpha


Theoretical massNumber of molelcules
Total (without water)185,8362
Polymers185,8362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)266.104, 266.104, 172.812
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 460 through 462 or (resid 464...
d_2ens_1(chain "B" and (resid 460 through 462 or (resid 464...
d_3ens_1(chain "C" and (resid 460 through 487 or (resid 489...
d_4ens_1(chain "D" and (resid 460 through 462 or (resid 464...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11THRTHRGLYGLYAA460 - 46258 - 60
d_12SERSERGLYGLYAA464 - 47262 - 70
d_13VALVALARGARGAA483 - 48781 - 85
d_14LYSLYSARGARGAA489 - 49487 - 92
d_15ASNASNGLNGLNAA504 - 517102 - 115
d_16ILEILEHISHISAA538 - 559136 - 157
d_17PROPROLEULEUAA562 - 565160 - 163
d_18LEULEUSERSERAA570 - 581168 - 179
d_19GLNGLNTHRTHRAA585 - 602183 - 200
d_110HISHISLYSLYSAA605 - 606203 - 204
d_111TRPTRPPHEPHEAA608 - 638206 - 236
d_112TYRTYRTYRTYRAA640238
d_113GLUGLUPHEPHEAA644 - 653242 - 251
d_114LYSLYSLEULEUAA655 - 678253 - 276
d_115LEULEUMETMETAA693 - 765291 - 363
d_116THRTHRVALVALAA767 - 776365 - 374
d_117SERSERPHEPHEAA778 - 790376 - 388
d_118THRTHRGLUGLUAA792 - 854390 - 452
d_119ILEILELYSLYSAA856 - 893454 - 491
d_120PHEPHEGLUGLUAA895 - 912493 - 510
d_121LEULEUGLUGLUAA926 - 941524 - 539
d_122LEULEUASPASPAA985 - 1188583 - 786
d_21THRTHRGLYGLYBB460 - 46258 - 60
d_22SERSERGLYGLYBB464 - 47262 - 70
d_23VALVALARGARGBB483 - 49481 - 92
d_24ASNASNGLNGLNBB504 - 517102 - 115
d_25ILEILEHISHISBB538 - 559136 - 157
d_26PROPROLEULEUBB562 - 565160 - 163
d_27LEULEUSERSERBB570 - 581168 - 179
d_28GLNGLNTYRTYRBB585 - 640183 - 238
d_29GLUGLUPHEPHEBB644 - 653242 - 251
d_210LYSLYSLEULEUBB655 - 678253 - 276
d_211LEULEUMETMETBB693 - 765291 - 363
d_212THRTHRVALVALBB767 - 776365 - 374
d_213SERSERPHEPHEBB778 - 790376 - 388
d_214THRTHRGLUGLUBB792 - 854390 - 452
d_215ILEILELYSLYSBB856 - 893454 - 491
d_216PHEPHEGLUGLUBB895 - 912493 - 510
d_217LEULEUGLUGLUBB926 - 941524 - 539
d_218LEULEUGLNGLNBB985 - 1095583 - 693
d_219PROPROASPASPBB1123 - 1188721 - 786
d_31THRTHRARGARGCC460 - 48758 - 85
d_32LYSLYSSERSERCC489 - 58187 - 179
d_33GLNGLNTHRTHRCC585 - 602183 - 200
d_34HISHISLYSLYSCC605 - 606203 - 204
d_35TRPTRPPHEPHECC608 - 638206 - 236
d_36TYRTYRPHEPHECC640 - 653238 - 251
d_37LYSLYSLEULEUCC655 - 678253 - 276
d_38LEULEUMETMETCC693 - 765291 - 363
d_39THRTHRVALVALCC767 - 776365 - 374
d_310SERSERPHEPHECC778 - 790376 - 388
d_311THRTHRGLUGLUCC792 - 854390 - 452
d_312ILEILELYSLYSCC856 - 893454 - 491
d_313PHEPHEGLUGLUCC895 - 912493 - 510
d_314LEULEUGLUGLUCC926 - 941524 - 539
d_315LEULEUGLNGLNCC985 - 1095583 - 693
d_316PROPROASPASPCC1123 - 1188721 - 786
d_41THRTHRGLYGLYDD460 - 46258 - 60
d_42SERSERGLYGLYDD464 - 47262 - 70
d_43VALVALARGARGDD483 - 48781 - 85
d_44LYSLYSARGARGDD489 - 49487 - 92
d_45ASNASNGLNGLNDD504 - 517102 - 115
d_46ILEILEHISHISDD538 - 559136 - 157
d_47PROPROLEULEUDD562 - 565160 - 163
d_48LEULEUSERSERDD570 - 581168 - 179
d_49GLNGLNTHRTHRDD585 - 602183 - 200
d_410HISHISLYSLYSDD605 - 606203 - 204
d_411TRPTRPPHEPHEDD608 - 638206 - 236
d_412TYRTYRTYRTYRDD640238
d_413GLUGLULEULEUDD644 - 678242 - 276
d_414LEULEUMETMETDD693 - 765291 - 363
d_415THRTHRASPASPDD767 - 1188365 - 786

NCS oper:
IDCodeMatrixVector
1given(-0.914884840439, 0.309199236905, -0.259579584391), (0.305394777789, 0.109518193903, -0.945906863757), (-0.2640449932, -0.944670099612, -0.194624367602)-73.8949275444, 78.3582265637, 67.8782487581
2given(0.173345820126, 0.158747261476, 0.971982784631), (-0.97033808386, -0.141332632766, 0.196135386727), (0.168508841476, -0.977151162251, 0.129539092382)-91.3841836845, -8.14159598453, 2.90541359653
3given(-0.36385867274, -0.846813123896, -0.387961853112), (0.791672574855, -0.500610241633, 0.350205539927), (-0.490776324302, -0.179713436255, 0.852550104295)-25.5727221549, 65.5518493297, -77.4200270096

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Components

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


Mass: 92917.750 Da / Num. of mol.: 4 / Fragment: UNP residues 430-1188
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOP2A, TOP2 / Production host: Escherichia coli (E. coli) / References: UniProt: P11388, EC: 5.99.1.3
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.17 Å3/Da / Density % sol: 61.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1M ammonium sulfate, 0.1M citrate (pH5.5), 12% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.67→23.19 Å / Num. obs: 128160 / % possible obs: 98.88 % / Redundancy: 2 % / Biso Wilson estimate: 51.47 Å2 / Rpim(I) all: 0.038 / Net I/σ(I): 16.99
Reflection shellResolution: 2.67→2.72 Å / Num. unique obs: 6358 / CC1/2: 0.772

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.67→23.19 Å / SU ML: 0.342 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 26.7988
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2478 2025 1.58 %
Rwork0.222 126106 -
obs0.2224 128131 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.19 Å2
Refinement stepCycle: LAST / Resolution: 2.67→23.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20516 0 15 382 20913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003320934
X-RAY DIFFRACTIONf_angle_d0.550928408
X-RAY DIFFRACTIONf_chiral_restr0.04133238
X-RAY DIFFRACTIONf_plane_restr0.00533655
X-RAY DIFFRACTIONf_dihedral_angle_d13.36732883
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.783918769469
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.739464969842
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.729311920499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.67-2.740.34371390.28958931X-RAY DIFFRACTION97.71
2.74-2.810.31521410.26968922X-RAY DIFFRACTION98.36
2.81-2.890.29621450.27449015X-RAY DIFFRACTION99.21
2.89-2.990.2951360.26719043X-RAY DIFFRACTION99.46
2.99-3.090.28041640.26259111X-RAY DIFFRACTION99.78
3.09-3.220.28981420.24779080X-RAY DIFFRACTION99.95
3.22-3.360.31121390.24739071X-RAY DIFFRACTION99.98
3.36-3.540.26951400.22819085X-RAY DIFFRACTION99.99
3.54-3.760.24471440.22739078X-RAY DIFFRACTION99.68
3.76-4.050.23111510.21288913X-RAY DIFFRACTION98.29
4.05-4.450.23331400.1959041X-RAY DIFFRACTION99
4.45-5.090.21651460.18739032X-RAY DIFFRACTION99.7
5.09-6.390.25631570.23079080X-RAY DIFFRACTION99.71
6.39-23.190.18721410.18878704X-RAY DIFFRACTION95.74
Refinement TLS params.Method: refined / Origin x: -44.9914235158 Å / Origin y: 30.3646682032 Å / Origin z: 6.73466764787 Å
111213212223313233
T0.295135649375 Å20.00625797375016 Å2-0.00433902998155 Å2-0.273361062953 Å20.0133834308867 Å2--0.475613714995 Å2
L0.234302600066 °20.0133057778574 °20.145226002754 °2-0.23901234057 °20.0397266135419 °2--0.333469771997 °2
S-0.0577589464484 Å °0.0351896426685 Å °0.0796307446987 Å °-0.0413463297911 Å °0.0354160304952 Å °0.141053489658 Å °-0.0413809611556 Å °0.00913917732105 Å °0.0267377518974 Å °
Refinement TLS groupSelection details: all

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