[English] 日本語
Yorodumi
- PDB-7qfn: Human Topoisomerase II Beta ATPase ADP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qfn
TitleHuman Topoisomerase II Beta ATPase ADP
ComponentsDNA topoisomerase 2-beta
KeywordsDNA BINDING PROTEIN / DNA Topoisomerase II Beta / Human / ATPase Domain / TOP2B
Function / homology
Function and homology information


positive regulation of single stranded viral RNA replication via double stranded DNA intermediate / sister chromatid segregation / resolution of meiotic recombination intermediates / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / positive regulation of double-strand break repair via nonhomologous end joining / cellular response to ATP / DNA topological change / SUMOylation of DNA replication proteins / ribonucleoprotein complex binding ...positive regulation of single stranded viral RNA replication via double stranded DNA intermediate / sister chromatid segregation / resolution of meiotic recombination intermediates / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / positive regulation of double-strand break repair via nonhomologous end joining / cellular response to ATP / DNA topological change / SUMOylation of DNA replication proteins / ribonucleoprotein complex binding / forebrain development / axonogenesis / B cell differentiation / neuron migration / cellular response to hydrogen peroxide / cellular senescence / ribonucleoprotein complex / chromatin binding / nucleolus / DNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytosol
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
ADENOSINE-5'-DIPHOSPHATE / DNA topoisomerase 2-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.621 Å
AuthorsLing, E.M. / Basle, A. / Cowell, I.G. / Blower, T.R. / Austin, C.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2022
Title: A comprehensive structural analysis of the ATPase domain of human DNA topoisomerase II beta bound to AMPPNP, ADP, and the bisdioxopiperazine, ICRF193.
Authors: Ling, E.M. / Basle, A. / Cowell, I.G. / van den Berg, B. / Blower, T.R. / Austin, C.A.
History
DepositionDec 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
Revision 2.0Mar 1, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Source and taxonomy
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_PDB_caveat / entity_src_gen / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_ls_restr / refine_ls_shell / software / struct_conf / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _entity_src_gen.gene_src_common_name / _pdbx_nonpoly_scheme.auth_seq_num ..._entity_src_gen.gene_src_common_name / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.dist / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_wR_factor_R_free / _refine.ls_wR_factor_R_work / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_average_fsc_free / _refine.pdbx_average_fsc_work / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.R_factor_all / _refine_ls_shell.pdbx_fsc_free / _refine_ls_shell.pdbx_fsc_work / _refine_ls_shell.wR_factor_R_work / _software.version / _struct_conn.pdbx_dist_value
Description: Chirality error / Provider: author / Type: Coordinate replacement
Revision 2.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA topoisomerase 2-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5825
Polymers45,9381
Non-polymers6444
Water23413
1
A: DNA topoisomerase 2-beta
hetero molecules

A: DNA topoisomerase 2-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,16310
Polymers91,8762
Non-polymers1,2878
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area6800 Å2
ΔGint-112 kcal/mol
Surface area31210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.021, 103.021, 66.693
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

-
Components

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


Mass: 45937.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOP2B / Production host: Escherichia coli (E. coli)
References: UniProt: Q02880, DNA topoisomerase (ATP-hydrolysing)
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulphate, 0.1 M bis tris (pH 5.5), 25 % w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.62→89.22 Å / Num. obs: 12596 / % possible obs: 100 % / Redundancy: 10.8 % / CC1/2: 0.997 / Net I/σ(I): 9
Reflection shellResolution: 2.62→2.74 Å / Redundancy: 11 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1513 / CC1/2: 0.78 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
DIALSdata reduction
xia2data reduction
MolProbitymodel building
pointlessdata scaling
Cootmodel building
Aimlessdata scaling
PHASERphasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1292119290

Resolution: 2.621→89.219 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.236 / WRfactor Rwork: 0.179 / SU B: 32.249 / SU ML: 0.3 / Average fsc free: 0.9473 / Average fsc work: 0.9677 / Cross valid method: FREE R-VALUE / ESU R: 1.673 / ESU R Free: 0.34
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2588 540 4.292 %
Rwork0.1993 12043 -
all0.202 --
obs-12583 99.929 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 60.189 Å2
Baniso -1Baniso -2Baniso -3
1-1.796 Å20.898 Å20 Å2
2--1.796 Å2-0 Å2
3----5.826 Å2
Refinement stepCycle: LAST / Resolution: 2.621→89.219 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2886 0 38 13 2937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122981
X-RAY DIFFRACTIONr_bond_other_d0.0020.0162747
X-RAY DIFFRACTIONr_angle_refined_deg1.9351.6464024
X-RAY DIFFRACTIONr_angle_other_deg0.6411.576419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2565357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.812511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.25110549
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.09910134
X-RAY DIFFRACTIONr_chiral_restr0.0830.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023270
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02579
X-RAY DIFFRACTIONr_nbd_refined0.2360.2617
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2060.22689
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21443
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0940.21642
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.289
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0320.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0040.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1480.216
X-RAY DIFFRACTIONr_nbd_other0.190.276
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3580.22
X-RAY DIFFRACTIONr_mcbond_it4.3984.5741437
X-RAY DIFFRACTIONr_mcbond_other4.3964.5751436
X-RAY DIFFRACTIONr_mcangle_it6.2426.8461791
X-RAY DIFFRACTIONr_mcangle_other6.2436.8471792
X-RAY DIFFRACTIONr_scbond_it5.2155.051544
X-RAY DIFFRACTIONr_scbond_other5.1795.0441536
X-RAY DIFFRACTIONr_scangle_it7.5767.3622233
X-RAY DIFFRACTIONr_scangle_other7.5577.3532222
X-RAY DIFFRACTIONr_lrange_it9.42455.3093335
X-RAY DIFFRACTIONr_lrange_other9.42355.3023336
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.621-2.6890.306460.3018650.3029130.9240.9399.78090.278
2.689-2.7620.354460.2798430.2838910.9190.94399.77550.263
2.762-2.8420.319130.2558620.2568760.9360.95699.88580.232
2.842-2.930.358390.2438170.2488570.8960.96199.88330.222
2.93-3.0260.368380.2337710.2388090.9340.9641000.21
3.026-3.1320.273460.2367490.2397950.9470.9641000.206
3.132-3.250.326250.2257290.2297540.9340.9661000.194
3.25-3.3820.307310.2127030.2167340.9280.971000.189
3.382-3.5320.211330.1856950.1867280.9660.9791000.165
3.532-3.7050.226230.176540.1726770.9680.9831000.153
3.705-3.9050.252240.1586190.1626430.9610.9851000.141
3.905-4.1410.222280.1555900.1586180.9710.9851000.137
4.141-4.4260.235210.145560.1435770.9720.9881000.13
4.426-4.780.182260.1525250.1545510.9810.9861000.142
4.78-5.2350.172210.1614730.1614940.980.9861000.153
5.235-5.850.278280.1834330.194630.9660.97999.5680.168
5.85-6.750.235190.2123920.2134110.9860.9731000.198
6.75-8.2550.313150.1943320.1983470.9510.9751000.189
8.255-11.6250.288100.2032700.2062800.9710.9741000.202
11.625-89.2190.25780.351650.3461740.980.93799.42530.353
Refinement TLS params.Method: refined / Origin x: 24.1147 Å / Origin y: 28.7573 Å / Origin z: 15.0194 Å
111213212223313233
T0.026 Å20.0169 Å20.0095 Å2-0.0611 Å20.0195 Å2--0.0424 Å2
L1.2156 °20.6744 °20.3695 °2-1.5242 °20.1786 °2--1.3959 °2
S0.0017 Å °0.0277 Å °0.1795 Å °-0.0513 Å °-0.0172 Å °0.1169 Å °-0.1433 Å °0.0543 Å °0.0155 Å °
Refinement TLS groupSelection: ALL

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more