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- EMDB-65775: Structure of transposase-activated RAG target capture complex wit... -

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Basic information

Entry
Database: EMDB / ID: EMD-65775
TitleStructure of transposase-activated RAG target capture complex with asymmetric linear target DNA (TCC-LA)
Map data
Sample
  • Complex: Transposase-activated RAG target capture complex with asymmetric linear target DNA
KeywordsRAG / Transposase / TCC / evolution / DNA BINDING PROTEIN
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsPang J / Zhang Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171250 China
CitationJournal: To Be Published
Title: Structural basis and dynamics of target capture and integration during cut-and-paste transposition
Authors: Pang J / Martin EC / Zheng X / Lu Q / Schatz DG / Zhang Y
History
DepositionAug 10, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65775.png

Downloads & links

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Map

FileDownload / File: emd_65775.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 280 pix.
= 268.8 Å		0.96 Å/pix.
x 280 pix.
= 268.8 Å		0.96 Å/pix.
x 280 pix.
= 268.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.318
Minimum - Maximum-0.4419217 - 1.1709864
Average (Standard dev.)0.00089034275 (±0.053963542)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 268.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_65775_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_65775_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 : Transposase-activated RAG target capture complex with asymmetric ...

EntireName: Transposase-activated RAG target capture complex with asymmetric linear target DNA
Components
  • Complex: Transposase-activated RAG target capture complex with asymmetric linear target DNA

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Supramolecule #1: Transposase-activated RAG target capture complex with asymmetric ...

SupramoleculeName: Transposase-activated RAG target capture complex with asymmetric linear target DNA
type: complex / ID: 1 / Parent: 0
Details: The M848E mutation was introduced into the transposase-activated RAG1.
Source (natural)Organism: Mus musculus (house mouse)

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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

Concentration0.2 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMKClPotassium chloride
2.0 mMMgCl2Magnesium chloride
20.0 mMHEPES4-(2-Hydroxyethyl)Piperazine-1-Ethan sulfonic Acid
0.5 mMTCEPTris(2-carboxyethyl)phosphine
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 282 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / 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: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 20010
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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