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- EMDB-61683: structure of phage T4 topoisomerase II central domain bound with DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-61683
Titlestructure of phage T4 topoisomerase II central domain bound with DNA
Map datasharp map
Sample
  • Complex: Phage T4 topoisomerase II central domian bound with G-segment DNA
    • Protein or peptide: DNA topoisomerase medium subunit
    • Protein or peptide: DNA topoisomerase large subunit,DNA topoisomerase small subunit
    • DNA: DNA (5'-D(P*TP*GP*TP*GP*TP*GP*TP*AP*TP*AP*TP*AP*TP*AP*CP*AP*CP*AP*TP*AP*TP*AP*TP*A)-3')
    • DNA: DNA (5'-D(P*AP*TP*AP*TP*AP*TP*GP*TP*GP*TP*AP*TP*AP*TP*AP*TP*AP*CP*AP*CP*AP*CP*AP*T)-3')
  • Ligand: MAGNESIUM ION
Keywordstopoisomerase II / ISOMERASE
Function / homology
Function and homology information


sister chromatid segregation / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / protein-containing complex / DNA binding / ATP binding
Similarity search - Function
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 ...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 / DNA topoisomerase, type IIA-like domain superfamily / 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 S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
DNA topoisomerase medium subunit / DNA topoisomerase large subunit / DNA topoisomerase small subunit
Similarity search - Component
Biological speciesEscherichia phage T4 (virus) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsChen YT / Xin YH / Xian RQ
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Sci Adv / Year: 2025
Title: Direct trapping of the transport-segment DNA by the central domain of type IIA topoisomerases.
Authors: Yuhui Xin / Runqi Xian / Congrong Liu / Oujia Zhang / Zihe Rao / Xuemei Li / Yutao Chen /
Abstract: Type IIA topoisomerases modulate DNA topology by coordinating the cleavage of gate-segment DNA and the passage of transport-segment DNA-a mechanism conserved across species and essential for diverse ...Type IIA topoisomerases modulate DNA topology by coordinating the cleavage of gate-segment DNA and the passage of transport-segment DNA-a mechanism conserved across species and essential for diverse cellular processes. While gate-segment interactions have been extensively studied, direct structural evidence of transport-segment capture has remained elusive, limiting our understanding of the full catalytic cycle. Here, we present a cryo-electron microscopy structure of the T4 bacteriophage topoisomerase II with a transport-segment DNA bound directly to its central domain. The structure reveals conformational rearrangements in the central domain that accommodate the transport-segment DNA, suggesting an alternative sequence of events in which the enzyme sliding along the loosely bound religated gate segment may precede transport-segment passage through the coiled-coil gate. Supported by mutational and biochemical assays, our findings provide previously unidentified mechanistic insights and open potential avenues for the development of next-generation type IIA topoisomerase inhibitors.
History
DepositionSep 25, 2024-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61683.png

Downloads & links

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Map

FileDownload / File: emd_61683.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharp map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 240 pix.
= 249.6 Å		1.04 Å/pix.
x 240 pix.
= 249.6 Å		1.04 Å/pix.
x 240 pix.
= 249.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.1534195 - 1.7119992
Average (Standard dev.)-0.00034210476 (±0.046719097)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 249.59999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map

Fileemd_61683_half_map_1.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map

Fileemd_61683_half_map_2.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Phage T4 topoisomerase II central domian bound with G-segment DNA

EntireName: Phage T4 topoisomerase II central domian bound with G-segment DNA
Components
  • Complex: Phage T4 topoisomerase II central domian bound with G-segment DNA
    • Protein or peptide: DNA topoisomerase medium subunit
    • Protein or peptide: DNA topoisomerase large subunit,DNA topoisomerase small subunit
    • DNA: DNA (5'-D(P*TP*GP*TP*GP*TP*GP*TP*AP*TP*AP*TP*AP*TP*AP*CP*AP*CP*AP*TP*AP*TP*AP*TP*A)-3')
    • DNA: DNA (5'-D(P*AP*TP*AP*TP*AP*TP*GP*TP*GP*TP*AP*TP*AP*TP*AP*TP*AP*CP*AP*CP*AP*CP*AP*T)-3')
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Phage T4 topoisomerase II central domian bound with G-segment DNA

SupramoleculeName: Phage T4 topoisomerase II central domian bound with G-segment DNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Escherichia phage T4 (virus)

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Macromolecule #1: DNA topoisomerase medium subunit

MacromoleculeName: DNA topoisomerase medium subunit / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA topoisomerase (ATP-hydrolysing)
Source (natural)Organism: Escherichia phage T4 (virus)
Molecular weightTheoretical: 51.951973 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQLNNRDLKS IIDNEALAYA MYTVENRAIP NMIDGFKPVQ RFVIARALDL ARGNKDKFHK LASIAGGVAD LGYHHGENSA QDAGALMAN TWNNNFPLLD GQGNFGSRTV QKAAASRYIF ARVSKNFYNV YKDTEYAPVH QDKEHIPPAF YLPIIPTVLL N GVSGIATG ...String:
MQLNNRDLKS IIDNEALAYA MYTVENRAIP NMIDGFKPVQ RFVIARALDL ARGNKDKFHK LASIAGGVAD LGYHHGENSA QDAGALMAN TWNNNFPLLD GQGNFGSRTV QKAAASRYIF ARVSKNFYNV YKDTEYAPVH QDKEHIPPAF YLPIIPTVLL N GVSGIATG YATYILPHSV SSVKKAVLQA LQGKKVTKPK VEFPEFRGEV VEIDGQYEIR GTYKFTSRTQ MHITEIPYKY DR ETYVSKI LDPLENKGFI TWDDACGEHG FGFKVKFRKE YSLSDNEEER HAKIMKDFGL IERRSQNITV INEKGKLQVY DNV VDLIKD FVEVRKTYVQ KRIDNKIKET ESAFRLAFAK AHFIKKVISG EIVVQGKTRK ELTEELSKID MYSSYVDKLV GMNI FHMTS DEAKKLAEEA KAKKEENEYW KTTDVVTEYT KDLEEIKHHH HHHHHHH

UniProtKB: DNA topoisomerase medium subunit

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Macromolecule #2: DNA topoisomerase large subunit,DNA topoisomerase small subunit

MacromoleculeName: DNA topoisomerase large subunit,DNA topoisomerase small subunit
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA topoisomerase (ATP-hydrolysing)
Source (natural)Organism: Escherichia phage T4 (virus)
Molecular weightTheoretical: 77.524703 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIKNEIKILS DIEHIKKRSG MYIGSSANET HERFMFGKWE SVQYVPGLVK LIDEIIDNSV DEGIRTKFKF ANKINVTIKN NQVTVEDNG RGIPQAMVKT PTGEEIPGPV AAWTIPKAGG NFGDDKERVT GGMNGVGSSL TNIFSVMFVG ETGDGQNNIV V RCSNGMEN ...String:
MIKNEIKILS DIEHIKKRSG MYIGSSANET HERFMFGKWE SVQYVPGLVK LIDEIIDNSV DEGIRTKFKF ANKINVTIKN NQVTVEDNG RGIPQAMVKT PTGEEIPGPV AAWTIPKAGG NFGDDKERVT GGMNGVGSSL TNIFSVMFVG ETGDGQNNIV V RCSNGMEN KSWEDIPGKW KGTRVTFIPD FMSFETNELS QVYLDITLDR LQTLAVVYPD IQFTFNGKKV QGNFKKYARQ YD EHAIVQE QENCSIAVGR SPDGFRQLTY VNNIHTKNGG HHIDCAMDDI CEDLIPQIKR KFKIDVTKAR VKECLTIVMF VRD MKNMRL IRQTKERLTS PFGEIRSHIQ LDAKKISRDI LNNEAILMPI IEAALARKLA AEKAAETKAA KKASKAKVHK HIKA NLCGK DADTTLFLTE GDSAIGYLID VRDKELHGGY PLRGKVLNSW GMSYADMLKN KELFDICAIT GLVLGEKAFE EKEDG EWFT FELNGDTIIV NENDEVQING KWITVGELRK NLMKFVKIDS SSVDMKKYKL QNNVRRSIKS SSMNYANVAI MTDADH DGL GSIYPSLLGF FSNWPELFEQ GRIRFVKTPV IIAQVGKKQE WFYTVAEYES AKDALPKHSI RYIKGLGSLE KSEYREM IQ NPVYDVVKLP ENWKELFEML MGDNADLRKE WMSQHHHHHH

UniProtKB: DNA topoisomerase large subunit, DNA topoisomerase small subunit

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Macromolecule #3: DNA (5'-D(P*TP*GP*TP*GP*TP*GP*TP*AP*TP*AP*TP*AP*TP*AP*CP*AP*CP*AP...

MacromoleculeName: DNA (5'-D(P*TP*GP*TP*GP*TP*GP*TP*AP*TP*AP*TP*AP*TP*AP*CP*AP*CP*AP*TP*AP*TP*AP*TP*A)-3')
type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.381813 KDa
SequenceString:
(DT)(DG)(DT)(DG)(DT)(DG)(DT)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DC)(DA)(DC)(DA)(DT)(DA) (DT)(DA)(DT)(DA)

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Macromolecule #4: DNA (5'-D(P*AP*TP*AP*TP*AP*TP*GP*TP*GP*TP*AP*TP*AP*TP*AP*TP*AP*CP...

MacromoleculeName: DNA (5'-D(P*AP*TP*AP*TP*AP*TP*GP*TP*GP*TP*AP*TP*AP*TP*AP*TP*AP*CP*AP*CP*AP*CP*AP*T)-3')
type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.350803 KDa
SequenceString:
(DA)(DT)(DA)(DT)(DA)(DT)(DG)(DT)(DG)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DC)(DA)(DC) (DA)(DC)(DA)(DT)

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 58418
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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