[English] 日本語
Yorodumi
- PDB-9o8p: CryoEM structure of M. mazei topoisomerase VI-minicircle DNA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9o8p
TitleCryoEM structure of M. mazei topoisomerase VI-minicircle DNA complex
Components
  • (Type 2 DNA topoisomerase 6 subunit ...) x 2
  • Minicircle DNA (arbitrary model sequence)
KeywordsISOMERASE/DNA / TOPRIM / GHKL / minicircle DNA / Spo11 / ISOMERASE-DNA complex
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / chromosome / magnesium ion binding / DNA binding / ATP binding
Similarity search - Function
DNA topoisomerase VI, subunit B, C-terminal / Type 2 DNA topoisomerase 6 subunit B C-terminal domain / DNA topoisomerase VI, subunit A / : / All-beta domain in DNA topoisomerase VI alpha subunit / Spo11/DNA topoisomerase VI subunit A / Spo11/DNA topoisomerase VI, subunit A, N-terminal / Topoisomerase 6 subunit A/Spo11, TOPRIM domain / Spo11/DNA topoisomerase VI subunit A superfamily / Type IIB DNA topoisomerase ...DNA topoisomerase VI, subunit B, C-terminal / Type 2 DNA topoisomerase 6 subunit B C-terminal domain / DNA topoisomerase VI, subunit A / : / All-beta domain in DNA topoisomerase VI alpha subunit / Spo11/DNA topoisomerase VI subunit A / Spo11/DNA topoisomerase VI, subunit A, N-terminal / Topoisomerase 6 subunit A/Spo11, TOPRIM domain / Spo11/DNA topoisomerase VI subunit A superfamily / Type IIB DNA topoisomerase / Topoisomerase 6 subunit A/Spo11, Toprim domain / Topoisomerase (Topo) IIB-type catalytic domain profile. / DNA topoisomerase VI, subunit B / DNA topoisomerase VI, subunit B, transducer / Topoisomerase VI B subunit, transducer / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S13-like, H2TH / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / DNA / DNA (> 10) / Type 2 DNA topoisomerase 6 subunit A / Type 2 DNA topoisomerase 6 subunit B
Similarity search - Component
Biological speciesMethanosarcina mazei Go1 (archaea)
unidentified (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsRichman, D.E. / Berger, J.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)5R35 CA263778 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1F32 GM128269 United States
CitationJournal: To Be Published
Title: Supercoiled DNA recognition and cleavage control in topoisomerase VI
Authors: Richman, D.E. / Wendorff, T.J. / Rashid, F. / Beck, C. / Yan, Q. / Johnson, H.R. / Eckerty, R.A. / Fogg, J.M. / Baker, M.L. / Zechiedrich, L. / Berger, J.M.
History
DepositionApr 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Type 2 DNA topoisomerase 6 subunit A
B: Type 2 DNA topoisomerase 6 subunit B
C: Type 2 DNA topoisomerase 6 subunit A
D: Type 2 DNA topoisomerase 6 subunit B
F: Minicircle DNA (arbitrary model sequence)
H: Minicircle DNA (arbitrary model sequence)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,80212
Polymers267,6636
Non-polymers1,1396
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Type 2 DNA topoisomerase 6 subunit ... , 2 types, 4 molecules ACBD

#1: Protein Type 2 DNA topoisomerase 6 subunit A / Type II DNA topoisomerase VI subunit A


Mass: 42179.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei Go1 (archaea)
Strain: ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88
Gene: top6A, MM_2418 / Plasmid: pST39 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8PUB7, DNA topoisomerase (ATP-hydrolysing)
#2: Protein Type 2 DNA topoisomerase 6 subunit B / Type II DNA topoisomerase VI subunit B / TopoVI-B


Mass: 68853.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei Go1 (archaea)
Strain: ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88
Gene: top6B, MM_2417 / Plasmid: pST39 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8PUB8, DNA topoisomerase (ATP-hydrolysing)

-
DNA chain , 1 types, 2 molecules FH

#3: DNA chain Minicircle DNA (arbitrary model sequence)


Mass: 22798.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli) / Strain (production host): ZYCY10P3S2T

-
Non-polymers , 3 types, 6 molecules

#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSourceDetails
1Topoisomerase VI heterotetramer (A2B2) bound to minicircle DNA and ADPNPCOMPLEX#1-#30MULTIPLE SOURCES
2Top6 heterotetramer (A2B2)COMPLEX#1-#21RECOMBINANT
3327 bp minicircle DNACOMPLEX#31RECOMBINANTApproximately 80 bp of the 327 bp minicircle are visible in EM imaging of the Top6-DNA complex
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.42 MDaNO
210.22 MDaYES
310.2 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
22Methanosarcina mazei Go1 (archaea)192952ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88
33unidentified (others)32644
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrainPlasmid
22Escherichia coli BL21(DE3) (bacteria)469008pST39
33Escherichia coli (E. coli)562ZYCY10P3S2T
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
250 mMpotassium glutamateC5H8KNO41
310 mMcalcium chlorideCaCl21
41 percent (v/v)glycerolC3H8O31
51 mMTCEPC9H15O6P1
61 mMADPNPC10H17N6O12P31
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Summary of order of assembly: minicircle DNA, Top6, then additional buffer components, ending with ADPNP. Sample was soluble and monodisperse.
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Au-flat 1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K / Details: Vitrification carried out in air

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Calibrated magnification: 130000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Calibrated defocus min: 800 nm / Calibrated defocus max: 2500 nm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 7 sec. / Electron dose: 46 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 11 / Num. of real images: 50906 / Details: ~80% collected at 30 degree stage tilt
EM imaging opticsEnergyfilter name: TFS Selectris

-
Processing

EM software
IDNameVersionCategory
1crYOLO1.9particle selection
2EPUimage acquisition
4cryoSPARC4.4.1CTF correction
7Coot0.9.8.91model fitting
8UCSF ChimeraX1.9model fitting
9ISOLDE1.9model fitting
11cryoSPARC4.4.1initial Euler assignment
12cryoSPARC4.4.1final Euler assignment
13cryoSPARC4.4.1classification
14cryoSPARC4.4.13D reconstruction
15EMReady23D reconstruction
16PHENIX1.21.1_5286model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 5216613
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 201073 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building

3D fitting-ID: 1

IDPDB-IDAccession codeInitial refinement model-IDSource nameTypeDetails
12Q2E

2q2e

2Q2E1PDBexperimental model
2OtherotherModelAngelo
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 139.49 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003918975
ELECTRON MICROSCOPYf_angle_d0.758726245
ELECTRON MICROSCOPYf_chiral_restr0.04832858
ELECTRON MICROSCOPYf_plane_restr0.00652877
ELECTRON MICROSCOPYf_dihedral_angle_d19.40377708

+
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