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- EMDB-39433: structure of phage T6 topoisomerase II ATPase domain bound with AMPPNP -

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Basic information

Entry
Database: EMDB / ID: EMD-39433
Titlestructure of phage T6 topoisomerase II ATPase domain bound with AMPPNP
Map dataT6ATPase half map
Sample
  • Complex: Phage T6 topoisomerase II ATPase domain bound with AMPPNP
    • Protein or peptide: DNA topoisomerase (ATP-hydrolyzing)
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
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 / DNA binding / ATP binding
Similarity search - Function
: / 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 ...: / 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)
Similarity search - Component
Biological speciesEnterobacteria phage T6 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.55 Å
AuthorsChen YT / Xin YH
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: To be published
Title: structure of phage T6 topoisomerase II ATPase domain bound with AMPPNP
Authors: Chen YT / Xin YH / Xian RQ
History
DepositionMar 12, 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_39433.png

Downloads & links

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Map

FileDownload / File: emd_39433.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationT6ATPase half map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 200 pix.
= 208. Å		1.04 Å/pix.
x 200 pix.
= 208. Å		1.04 Å/pix.
x 200 pix.
= 208. 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: 0.45
Minimum - Maximum-1.8582549 - 2.302831
Average (Standard dev.)0.00037716815 (±0.050806087)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 208.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: T6ATPase half map

Fileemd_39433_half_map_1.map
AnnotationT6ATPase half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: T6ATPase half map

Fileemd_39433_half_map_2.map
AnnotationT6ATPase 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 topoisomerase II ATPase domain bound with AMPPNP

EntireName: Phage T6 topoisomerase II ATPase domain bound with AMPPNP
Components
  • Complex: Phage T6 topoisomerase II ATPase domain bound with AMPPNP
    • Protein or peptide: DNA topoisomerase (ATP-hydrolyzing)
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Phage T6 topoisomerase II ATPase domain bound with AMPPNP

SupramoleculeName: Phage T6 topoisomerase II ATPase domain bound with AMPPNP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Enterobacteria phage T6 (virus)

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Macromolecule #1: DNA topoisomerase (ATP-hydrolyzing)

MacromoleculeName: DNA topoisomerase (ATP-hydrolyzing) / type: protein_or_peptide / ID: 1 / 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 #2: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 2 / 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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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / 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: 2.0 µm / Nominal defocus min: 1.2 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: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 80615
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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