[English] 日本語
Yorodumi
- PDB-4r1f: Re-refined Human DNA topoisomerase IIa (ATPase and transducer dom... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4r1f
TitleRe-refined Human DNA topoisomerase IIa (ATPase and transducer domains) in complex with ADP and SO4
ComponentsDNA topoisomerase 2-alpha
KeywordsISOMERASE / Human topoisomerase IIA
Function / homology
Function and homology information


apoptotic chromosome condensation / positive regulation of single stranded viral RNA replication via double stranded DNA intermediate / sister chromatid segregation / resolution of meiotic recombination intermediates / female meiotic nuclear division / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / embryonic cleavage / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / Transcription of E2F targets under negative control by DREAM complex / DNA binding, bending ...apoptotic chromosome condensation / positive regulation of single stranded viral RNA replication via double stranded DNA intermediate / sister chromatid segregation / resolution of meiotic recombination intermediates / female meiotic nuclear division / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / embryonic cleavage / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / Transcription of E2F targets under negative control by DREAM complex / DNA binding, bending / DNA topoisomerase (ATP-hydrolysing) / 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 / chromatin organization / 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 / Ribosomal Protein S5; domain 2 - #10 / Toprim domain profile. / TOPRIM domain / Ribosomal Protein S5; domain 2 / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / DNA topoisomerase 2-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsStanger, F.V. / Schirmer, T.
Citation
Journal: Plos One / Year: 2014
Title: Structure of the N-Terminal Gyrase B Fragment in Complex with ADPPi Reveals Rigid-Body Motion Induced by ATP Hydrolysis
Authors: Stanger, F.V. / Dehio, C. / Schirmer, T.
#1: Journal: J.Biol.Chem. / Year: 2005
Title: NUCLEOTIDE-DEPENDENT DOMAIN MOVEMENT in THE ATPASE DOMAIN of A HUMAN TYPE IIA DNA TOPOISOMERASE
Authors: Wei, H. / Ruthenburg, A.J. / Bechis, S.K. / Verdine, G.L.
History
DepositionAug 5, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Other
Revision 1.2Nov 8, 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 0THIS ENTRY 4R1F REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R1ZXNSF) ...THIS ENTRY 4R1F REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R1ZXNSF) DETERMINED BY AUTHORS OF THE PDB ENTRY 1ZXN: AUTHOR INITIALS, AUTHOR LAST NAME

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)184,82816
Polymers182,6424
Non-polymers2,18612
Water2,414134
1
A: DNA topoisomerase 2-alpha
B: DNA topoisomerase 2-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4128
Polymers91,3212
Non-polymers1,0916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-68 kcal/mol
Surface area32870 Å2
MethodPISA
2
C: DNA topoisomerase 2-alpha
D: DNA topoisomerase 2-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4168
Polymers91,3212
Non-polymers1,0956
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6760 Å2
ΔGint-92 kcal/mol
Surface area33540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.015, 90.492, 148.293
Angle α, β, γ (deg.)90.000, 89.970, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNAA29 - 4221 - 394
21GLNGLNBB29 - 4221 - 394
12GLNGLNAA29 - 4221 - 394
22GLNGLNCC29 - 4221 - 394
13GLNGLNAA29 - 4221 - 394
23GLNGLNDD29 - 4221 - 394
14ASNASNBB29 - 4241 - 396
24ASNASNCC29 - 4241 - 396
15ASNASNBB29 - 4241 - 396
25ASNASNDD29 - 4241 - 396
16LYSLYSCC29 - 4251 - 397
26LYSLYSDD29 - 4251 - 397

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

-
Protein , 1 types, 4 molecules ABCD

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


Mass: 45660.535 Da / Num. of mol.: 4 / Fragment: UNP residues 29-428
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOP2, TOP2A / Plasmid: pSB23 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: P11388, EC: 5.99.1.3

-
Non-polymers , 5 types, 146 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.85 % / Description: AUTHORS USED SF DATA FROM THE ENTRY 1ZXN.

-
Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

Software
NameVersionClassificationNB
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZXN

1zxn


Resolution: 2.51→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.929 / SU B: 10.968 / SU ML: 0.236 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.733 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2434 4648 7.6 %RANDOM
Rwork0.2081 ---
all0.2108 61079 --
obs0.2108 61079 94.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 186.07 Å2 / Biso mean: 64.255 Å2 / Biso min: 32.38 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20 Å2-0.63 Å2
2--0.56 Å20 Å2
3----1.58 Å2
Refinement stepCycle: LAST / Resolution: 2.51→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12093 0 133 134 12360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01912484
X-RAY DIFFRACTIONr_bond_other_d0.0060.0212041
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.9616809
X-RAY DIFFRACTIONr_angle_other_deg1.223327734
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.13951488
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.68524.991567
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.78152329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7741552
X-RAY DIFFRACTIONr_chiral_restr0.0840.21862
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213798
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022842
X-RAY DIFFRACTIONr_mcbond_it4.8656.0995994
X-RAY DIFFRACTIONr_mcbond_other4.8656.0995993
X-RAY DIFFRACTIONr_mcangle_it6.8729.1457468
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A216380.12
12B216380.12
21A214590.12
22C214590.12
31A211410.12
32D211410.12
41B225800.11
42C225800.11
51B218270.12
52D218270.12
61C218040.12
62D218040.12
LS refinement shellResolution: 2.51→2.576 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 281 -
Rwork0.279 3512 -
all-3793 -
obs--80.39 %

+
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