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- EMDB-47256: DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap a... -

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Basic information

Entry
Database: EMDB / ID: EMD-47256
TitleDNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-5.5 (consensus)
Map data
Sample
  • Complex: D_1000285903
KeywordsNucleosome / DNA polymerase Beta / DNA Repair / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsWeaver TM / Ryan BJ / Freudenthal BD
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM128562 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32 GM140718 United States
CitationJournal: To Be Published
Title: DNA polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-5.5
Authors: Ryan BJ / Weaver TM / Freudenthal BD
History
DepositionOct 9, 2024-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47256.png

Downloads & links

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Map

FileDownload / File: emd_47256.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 320 pix.
= 310.4 Å		0.97 Å/pix.
x 320 pix.
= 310.4 Å		0.97 Å/pix.
x 320 pix.
= 310.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.18191323 - 0.3872193
Average (Standard dev.)0.00035750412 (±0.01409344)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 310.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_47256_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_47256_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 : D_1000285903

EntireName: D_1000285903
Components
  • Complex: D_1000285903

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Supramolecule #1: D_1000285903

SupramoleculeName: D_1000285903 / 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: 7.1
Component:
ConcentrationNameFormula
25.0 mMN-2-hydroxyethylpiperazine-N-2-ethane sulfonic acid
50.0 mMSodium ChlorideNaCl
1.0 mMTris (2-carboxyethyl) phosphine hydrochloride
5.0 mMEthylenediaminetetraacetic acid

Details: 25mM HEPES (pH-7.1), 50mM NaCl, 1mM TCEP, and 5mM EDTA
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsDNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-5.5

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Electron microscopy

MicroscopeTFS KRIOS
Details300 kV FEI Titan Krios G3i cryo-TEM equipped with a Falcon 4 direct electron detector and Selectris energy filter
Image recordingFilm or detector model: FEI FALCON IV (4k 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: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7u51

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 7167
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.3.1)

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