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- EMDB-72647: Focused refinement map of distal right end DNA region within IF3A... -

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Basic information

Entry
Database: EMDB / ID: EMD-72647
TitleFocused refinement map of distal right end DNA region within IF3A transposase complex with synapsed ends
Map data
Sample
  • Complex: 1F3A-transposase complex with paired transposon ends
KeywordsNucleic acid binding / DNA integration / Transposon / CRISPR / DNA BINDING PROTEIN / CAST
Biological speciesVibrio cholerae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.94 Å
AuthorsTruong VH / Miller DJ / Fatma S / Kellogg EH
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F31GM151863 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM144566 United States
CitationJournal: To Be Published
Title: Structural basis of end recognition and pairing by I-F3 CRISPR-associated transposon
Authors: Truong VH / Fatma S / Miller DJ / Kellogg EH
History
DepositionSep 9, 2025-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72647.png

Downloads & links

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Map

FileDownload / File: emd_72647.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.26 Å/pix.
x 256 pix.
= 322.56 Å		1.26 Å/pix.
x 256 pix.
= 322.56 Å		1.26 Å/pix.
x 256 pix.
= 322.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.26 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.458
Minimum - Maximum-0.00006151986 - 1.0010645
Average (Standard dev.)0.37617776 (±0.009801847)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 322.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_72647_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_72647_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 : 1F3A-transposase complex with paired transposon ends

EntireName: 1F3A-transposase complex with paired transposon ends
Components
  • Complex: 1F3A-transposase complex with paired transposon ends

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Supramolecule #1: 1F3A-transposase complex with paired transposon ends

SupramoleculeName: 1F3A-transposase complex with paired transposon ends / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 694 KDa

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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
Component:
ConcentrationFormulaName
26.0 mMC8H18N2O4SHepes
5.0 mMC4H11NO3HClTris hydrochloride
20.0 mMKClPotassium chloride
150.0 mMNaClSodium chloride
0.2 mMMgCl2Magnesium chloride
15.0 mMMgOAcMagnesium acetate
2.0 percentC3H8O3Glycerol
1.0 mMC10H16N5O13P3ATP
1.0 mMC4H10O2S2DTT
0.1 percentC58H114O26Tween-20
10.0 mMC10H16N2O3SBiotin
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 89094
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.94 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 89094
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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