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- PDB-9o8z: CryoEM structure of M. mazei topoisomerase VI-minicircle DNA comp... -

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Basic information

Entry
Database: PDB / ID: 9o8z
TitleCryoEM structure of M. mazei topoisomerase VI-minicircle DNA complex in partially unfolded transducer state
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 / DNA replication / 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 / 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: 4 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: Nat Commun / Year: 2026
Title: Supercoiled DNA recognition and cleavage control in topoisomerase VI.
Authors: Daniel E Richman / Timothy J Wendorff / Fahad Rashid / Curtis Beck / Qianyun Yan / Haley R Johnson / Ryan A Eckerty / Jonathan M Fogg / Matthew L Baker / Lynn Zechiedrich / James M Berger /
Abstract: Type II topoisomerases modulate DNA supercoiling and resolve chromosome entanglements. Type IIB topoisomerases, exemplified by DNA topoisomerase VI (Top6), are used by plants and archaea to support ...Type II topoisomerases modulate DNA supercoiling and resolve chromosome entanglements. Type IIB topoisomerases, exemplified by DNA topoisomerase VI (Top6), are used by plants and archaea to support endoreduplication and cell proliferation, respectively; homologs of Top6 further serve to initiate meiotic recombination in eukaryotes and constitute the nuclease portion of MksBEFG/Wadjet/Gabija bacterial defense systems. To understand how such factors act upon DNA, we determine structures of Top6 bound to supercoiled minicircles in cleaved and uncleaved states using single-particle electron cryo-microscopy. The structures show that Top6 binds a curved 74 bp region of the supercoiled minicircle DNA and that it cuts at a distinct deformability motif, explaining its preference for supercoiled substrates and highlighting the role of DNA plasticity in cleavage site selection. Dynamic protein-DNA interactions and an unanticipated tension sensor help recognize bent DNA and couple ATPase disposition to cleavage state activation. Our observations explain how DNA recognition and cleavage by type II topoisomerases are regulated by interdependent structural changes in DNA and the enzyme.
History
DepositionApr 17, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)268,82613
Polymers267,6636
Non-polymers1,1647
Water00
1


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

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Components

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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)

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DNA chain , 1 types, 2 molecules FH

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


Mass: 22798.822 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

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Non-polymers , 3 types, 7 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: 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
#6: Chemical ChemComp-K / POTASSIUM ION


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

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

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

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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

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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

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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
11PHENIX1.21.1_5286model refinement
12cryoSPARC4.4.1initial Euler assignment
13cryoSPARC4.4.1final Euler assignment
14cryoSPARC4.4.1classification
15cryoSPARC4.4.13D reconstruction
16EMReady23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 5216613
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 176843 / 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: 158.67 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004918900
ELECTRON MICROSCOPYf_angle_d0.938126146
ELECTRON MICROSCOPYf_chiral_restr0.05222850
ELECTRON MICROSCOPYf_plane_restr0.00842862
ELECTRON MICROSCOPYf_dihedral_angle_d20.33147673

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