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- EMDB-49247: A Ligation complex in NHEJ pathway (AMP-Lys and AMP-DNA mix states) -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-49247
TitleA Ligation complex in NHEJ pathway (AMP-Lys and AMP-DNA mix states)
Map dataComposite Map of Focused maps generated by Combine Focused Maps in PHENIX
Sample
  • Complex: A Ligation complex in NHEJ pathway
KeywordsNHEJ / ligation / XLF / PAXX / DNA repair / Ligase IV / LIGASE-TRANSFERASE-DNA complex / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsLi J / Liu L / Gellert M / Yang W
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: To Be Published
Title: A Ligation complex in NHEJ pathway (AMP-Lys and AMP-DNA mix states)
Authors: Li J / Liu L / Gellert M / Yang W
History
DepositionFeb 15, 2025-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49247.png

Downloads & links

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Map

FileDownload / File: emd_49247.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite Map of Focused maps generated by Combine Focused Maps in PHENIX
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 426.496 Å		0.83 Å/pix.
x 512 pix.
= 426.496 Å		0.83 Å/pix.
x 512 pix.
= 426.496 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.833 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.0
Minimum - Maximum-29.222507 - 68.17886
Average (Standard dev.)0.0031534133 (±1.4311503)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 426.496 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Composite map sharpened by DeepEMhancer

Fileemd_49247_additional_1.map
AnnotationComposite map sharpened by DeepEMhancer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Composite half A Map of Focused half maps...

Fileemd_49247_half_map_1.map
AnnotationComposite half A Map of Focused half maps generated by Combine Focused Maps in PHENIX
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Composite half B Map of Focused half maps...

Fileemd_49247_half_map_2.map
AnnotationComposite half B Map of Focused half maps generated by Combine Focused Maps in PHENIX
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : A Ligation complex in NHEJ pathway

EntireName: A Ligation complex in NHEJ pathway
Components
  • Complex: A Ligation complex in NHEJ pathway

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Supramolecule #1: A Ligation complex in NHEJ pathway

SupramoleculeName: A Ligation complex in NHEJ pathway / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 854 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

Concentration0.35 mg/mL
BufferpH: 7.9
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 47.39 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE / Details: ab initio reconstituted by cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF
Details: The Combine_Focused_Maps in Phenix was used to generate the composite map as well as two half maps. The two half maps were used to calculate the resolution in PostProcess in RELION.
Number images used: 434181
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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