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- EMDB-45095: Focused map of TnsABCD transpososome -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-45095
TitleFocused map of TnsABCD transpososome
Map data
Sample
  • Complex: TnsABCD-DNA complex
    • Complex: TnsABCD
    • Complex: DNA
KeywordsTn7-like transposon / type I-B2 CAST / DNA binding protein / transpososome
Biological speciesPeltigera membranacea (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsChang L / Wang S
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Structure of TnsABCD transpososome
Authors: Chang L / Wang S
History
DepositionMay 27, 2024-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45095.png

Downloads & links

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Map

FileDownload / File: emd_45095.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 480 pix.
= 394.56 Å		0.82 Å/pix.
x 480 pix.
= 394.56 Å		0.82 Å/pix.
x 480 pix.
= 394.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0576
Minimum - Maximum-0.14840126 - 0.37882188
Average (Standard dev.)0.00072551967 (±0.011231552)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 394.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_45095_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_45095_half_map_2.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 : TnsABCD-DNA complex

EntireName: TnsABCD-DNA complex
Components
  • Complex: TnsABCD-DNA complex
    • Complex: TnsABCD
    • Complex: DNA

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Supramolecule #1: TnsABCD-DNA complex

SupramoleculeName: TnsABCD-DNA complex / type: complex / ID: 1 / Parent: 0

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Supramolecule #2: TnsABCD

SupramoleculeName: TnsABCD / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Peltigera membranacea (fungus)

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Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Peltigera membranacea (fungus) / Synthetically produced: Yes

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.0 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: 0.8 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 38326
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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