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- EMDB-75532: DNA Ligase IIIa bound to nucleosome containing a nick at SHL-2 (L... -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-75532
TitleDNA Ligase IIIa bound to nucleosome containing a nick at SHL-2 (LigIIIa/DNA local refine)
Map data
Sample
  • Complex: DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-2
KeywordsNucleosome / DNA Ligase IIIa / DNA Repair / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsBoesch DJ / Weaver TM
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: DNA Ligase IIIa bound to nucleosome containing a nick at SHL-2
Authors: Boesch DJ / Weaver TM
History
DepositionFeb 12, 2026-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75532.png

Downloads & links

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Map

FileDownload / File: emd_75532.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 400 pix.
= 260.8 Å		0.65 Å/pix.
x 400 pix.
= 260.8 Å		0.65 Å/pix.
x 400 pix.
= 260.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.652 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.028102053 - 0.13309728
Average (Standard dev.)0.00024218552 (±0.0028328423)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 260.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_75532_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_75532_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 : DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-2

EntireName: DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-2
Components
  • Complex: DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-2

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Supramolecule #1: DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-2

SupramoleculeName: DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-2
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3l2p

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 50548
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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