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- EMDB-39454: structure of phage T6 full-length topoisomerase II bound with DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-39454
Titlestructure of phage T6 full-length topoisomerase II bound with DNA
Map dataT6 Topoisomerase II full-length bound with DNA map
Sample
  • Complex: Phage T6 full-length topoisomerase II bound with DNA
    • Protein or peptide: DNA topoisomerase medium subunit
    • Protein or peptide: DNA topoisomerase (ATP-hydrolyzing)
    • DNA: DNA (50-MER)
    • DNA: DNA (50-MER)
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Keywordstopoisomerase II / ISOMERASE
Function / homology
Function and homology information


sister chromatid segregation / 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
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 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 (ATP-hydrolyzing) / DNA topoisomerase medium subunit
Similarity search - Component
Biological speciesEnterobacteria phage T6 (virus) / Escherichia phage T4 (virus) / DNA molecule (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.73 Å
AuthorsChen YT / Xin YH / Xian RQ
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: To be published
Title: structure of phage T6 full-length topoisomerase II bound with DNA
Authors: Chen YT / Xin YH / Xian RQ
History
DepositionMar 13, 2024-
Header (metadata) releaseSep 25, 2024-
Map releaseSep 25, 2024-
UpdateSep 25, 2024-
Current statusSep 25, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39454.png

Downloads & links

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Map

FileDownload / File: emd_39454.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationT6 Topoisomerase II full-length bound with DNA map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. 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: 0.1
Minimum - Maximum-0.8516143 - 1.177926
Average (Standard dev.)0.0008344372 (±0.040449176)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: T6 Topoisomerase II full-length bound with DNA half map

Fileemd_39454_half_map_1.map
AnnotationT6 Topoisomerase II full-length bound with DNA half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: T6 Topoisomerase II full-length bound with DNA half map

Fileemd_39454_half_map_2.map
AnnotationT6 Topoisomerase II full-length bound with DNA half 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 T6 full-length topoisomerase II bound with DNA

EntireName: Phage T6 full-length topoisomerase II bound with DNA
Components
  • Complex: Phage T6 full-length topoisomerase II bound with DNA
    • Protein or peptide: DNA topoisomerase medium subunit
    • Protein or peptide: DNA topoisomerase (ATP-hydrolyzing)
    • DNA: DNA (50-MER)
    • DNA: DNA (50-MER)
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

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Supramolecule #1: Phage T6 full-length topoisomerase II bound with DNA

SupramoleculeName: Phage T6 full-length topoisomerase II bound with DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Enterobacteria phage T6 (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 (ATP-hydrolyzing)

MacromoleculeName: DNA topoisomerase (ATP-hydrolyzing) / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA topoisomerase (ATP-hydrolysing)
Source (natural)Organism: Enterobacteria phage T6 (virus)
Molecular weightTheoretical: 69.237289 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIKNEIKILS DIEHIKKRSG MYIGSSANEM HERFLFGKWE SVQYVPGLVK LIDEIIDNSV DEGIRTKFKF ANKINVTIKN NQVTVEDNG RGIPQAMVKT PTGEEIPGPV AAWTIPKAGG NFGDDKERVT GGMNGVGSSL TNIFSVMFVG ETGDGQNNIV V RCSNGMEN ...String:
MIKNEIKILS DIEHIKKRSG MYIGSSANEM HERFLFGKWE SVQYVPGLVK LIDEIIDNSV DEGIRTKFKF ANKINVTIKN NQVTVEDNG RGIPQAMVKT PTGEEIPGPV AAWTIPKAGG NFGDDKERVT GGMNGVGSSL TNIFSVMFVG ETGDGQNNIV V RCSNGMEN KSWETIPGKW KGTRVTFIPD FMSFETNELS QVYLDITLDR LQTLAVVYPD IQFTFNGKKV QGNFKKYARQ YD EHAIVQE QENCSIAVGR SPDGFRQLTY VNNIHTKNGG HHIDCVMDDI CEDLIPQIKR KFKIDVTKAR VKECLTIVMF VRD MKNMRF DSQTKERLTS PFGEIRSHIQ LDAKKISRAI LNNEAILMPI IEAALARKLA AEKAAETKAA KKASKAKVHK HIKA NLCGK DADTTLFLTE GDSAIGYLID VRDKELHGGY PLRGKVLNSW GMSYADMLKN KELFDICAIT GLVLGEKAEN LNYHN IAIM TDADHDGLGS IYPSLLGFFS NWPELFEQGR IRFVKTPVII AHVGKKQEWF YTVAEYESAK DALPKHSIRY IKGLGS LEK SEYREMIQNP VYDVVKLPEN WKELFEMLMG DNADLRKEWM SQHHHHHH

UniProtKB: DNA topoisomerase (ATP-hydrolyzing)

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Macromolecule #3: DNA (50-MER)

MacromoleculeName: DNA (50-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 16.058391 KDa
SequenceString: (DA)(DT)(DG)(DC)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DG)(DT) (DA)(DT)(DG)(DT)(DG)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DC)(DA)(DC)(DA) (DT) (DA)(DT)(DA)(DT)(DA)(DT) ...String:
(DA)(DT)(DG)(DC)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DG)(DT) (DA)(DT)(DG)(DT)(DG)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DC)(DA)(DC)(DA) (DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)

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Macromolecule #4: DNA (50-MER)

MacromoleculeName: DNA (50-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 15.965361 KDa
SequenceString: (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DG)(DT)(DG)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DC)(DA)(DC)(DA) (DC)(DA)(DT)(DA)(DC)(DA)(DT)(DA)(DT)(DA) (DC) (DA)(DT)(DA)(DT)(DA)(DT) ...String:
(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DG)(DT)(DG)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DC)(DA)(DC)(DA) (DC)(DA)(DT)(DA)(DC)(DA)(DT)(DA)(DT)(DA) (DC) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DG)(DC)(DA)(DT)

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Macromolecule #5: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 5 / Number of copies: 2 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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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

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.73 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 11206
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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