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- EMDB-31748: Negative-staining map of T4 DNA ligase-AMP-DNA Ternary Complex III -

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Basic information

Entry
Database: EMDB / ID: EMD-31748
TitleNegative-staining map of T4 DNA ligase-AMP-DNA Ternary Complex III
Map dataT4 DNA ligase binding nick double-stranded DNA complex conformation Bent II
Sample
  • Complex: T4 DNA ligase binding nick double-stranded DNA complex conformation Bent II
KeywordsLigase / Complex / DNA Repair / DNA replication / DNA BINDING PROTEIN
Biological speciesbacteriophage T (virus)
Methodsingle particle reconstruction / negative staining / Resolution: 13.4 Å
AuthorsZhang L / Li N
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)11922410 China
CitationJournal: To Be Published
Title: Repair of DNA nick by T4 DNA ligase in three parallel pathways
Authors: Zhang L / Li N
History
DepositionAug 20, 2021-
Header (metadata) releaseAug 24, 2022-
Map releaseAug 24, 2022-
UpdateSep 13, 2023-
Current statusSep 13, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31748.png

Downloads & links

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Map

FileDownload / File: emd_31748.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationT4 DNA ligase binding nick double-stranded DNA complex conformation Bent II
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.61 Å/pix.
x 100 pix.
= 160.7 Å		1.61 Å/pix.
x 100 pix.
= 160.7 Å		1.61 Å/pix.
x 100 pix.
= 160.7 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.607 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0424
Minimum - Maximum-0.00073035434 - 0.19692646
Average (Standard dev.)0.004961783 (±0.021072734)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-50
Dimensions100100100
Spacing100100100
CellA=B=C: 160.7 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : T4 DNA ligase binding nick double-stranded DNA complex conformati...

EntireName: T4 DNA ligase binding nick double-stranded DNA complex conformation Bent II
Components
  • Complex: T4 DNA ligase binding nick double-stranded DNA complex conformation Bent II

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Supramolecule #1: T4 DNA ligase binding nick double-stranded DNA complex conformati...

SupramoleculeName: T4 DNA ligase binding nick double-stranded DNA complex conformation Bent II
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: bacteriophage T (virus)
Molecular weightTheoretical: 55 KDa

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.011 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
100.0 mMNaClSodium chloride
10.0 mMMgCl2Magnesium chloride
10.0 mMDTTDithiothreitol
0.3 mMATPadenosine-triphosphate
50.0 mMTris-HClTris(Hydroxymethyl)aminomethane
StainingType: NEGATIVE / Material: Uranyl Acetate
Details: A 4.0 uL drop of the sample was placed on a glow-discharged EM specimen grid (CF200-Cu, Electron Microscopy Sciences, Hatfield, PA, USA) with a thin carbon film for 1 min and the excess ...Details: A 4.0 uL drop of the sample was placed on a glow-discharged EM specimen grid (CF200-Cu, Electron Microscopy Sciences, Hatfield, PA, USA) with a thin carbon film for 1 min and the excess solution was blotted with filter paper. Then, the grid was washed with a clean drop (~35 uL/drop) of water and stained two times with two drops (~25 uL/drop) of 2% (w/v) uranyl acetate (UA) for 10 s, 30 s respectively before air-drying.
GridModel: C-flat / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.038 kPa
DetailsT4 DNA ligase and nicked double-stranded DNA substrate were mixed at a molar ratio of 1:1

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Electron microscopy

MicroscopeTFS TALOS F200C
Image recordingFilm or detector model: FEI CETA (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 3765 / Average exposure time: 1.0 sec. / Average electron dose: 160.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 9204
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 13.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 596
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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