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- EMDB-45862: Focused map of XLF in ligation complex like in the NHEJ pathway -

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Basic information

Entry
Database: EMDB / ID: EMD-45862
TitleFocused map of XLF in ligation complex like in the NHEJ pathway
Map dataFocused map of XLF in the ligation complex II
Sample
  • Complex: Ligation complex like in the NHEJ pathway
    • Protein or peptide: human XLF
KeywordsNHEJ / ligation / XLF / PAXX / DNA repair / Ligase IV / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 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: The ligation complex like in the NHEJ pathway
Authors: Li J / Liu L / Gellert M / Yang W
History
DepositionJul 22, 2024-
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_45862.png

Downloads & links

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Map

FileDownload / File: emd_45862.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused map of XLF in the ligation complex II
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: 0.3
Minimum - Maximum-0.45748898 - 1.1947224
Average (Standard dev.)-0.0005831755 (±0.023017317)
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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Mask #1

Fileemd_45862_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half 1 map

Fileemd_45862_half_map_1.map
Annotationhalf 1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half 2 map

Fileemd_45862_half_map_2.map
Annotationhalf 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 : Ligation complex like in the NHEJ pathway

EntireName: Ligation complex like in the NHEJ pathway
Components
  • Complex: Ligation complex like in the NHEJ pathway
    • Protein or peptide: human XLF

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Supramolecule #1: Ligation complex like in the NHEJ pathway

SupramoleculeName: Ligation complex like in the NHEJ pathway / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 854 KDa

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Macromolecule #1: human XLF

MacromoleculeName: human XLF / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPVMEELEQG LLMQPWAWLQ LAENSLLAKV FITKQGYALL VSDLQQVWHE QVDTSVVSQR AKE LNKRLT APPAAFLCHL DNLLRPLLKD AAHPSEATFS CDCVADALIL RVRSELSGLP FYWN FHCML ASPSLVSQHL IRPLMGMSLA LQCQVRELAT LLHMKDLEIQ ...String:
GPVMEELEQG LLMQPWAWLQ LAENSLLAKV FITKQGYALL VSDLQQVWHE QVDTSVVSQR AKE LNKRLT APPAAFLCHL DNLLRPLLKD AAHPSEATFS CDCVADALIL RVRSELSGLP FYWN FHCML ASPSLVSQHL IRPLMGMSLA LQCQVRELAT LLHMKDLEIQ DYQESGATLI RDRLK TEPF EENSFLEQFM IEKLPEACSI GDGKPFVMNL QDLYMAVTTQ EVQVGQKHQG AGDPHT SNS ASLQGIDSQC VNQPEQLVSS APTLSAPEKE STGTSGPLQR PQLSKVKRKK PRGLFS

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 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: EMDB MAP
EMDB ID:

23509

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 133163
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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