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- EMDB-19252: DNA-PKcs local refinement of telomeric RAP1:DNA-PK complex -

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Basic information

Entry
Database: EMDB / ID: EMD-19252
TitleDNA-PKcs local refinement of telomeric RAP1:DNA-PK complex
Map data
Sample
  • Complex: Telomeric RAP1:DNA-PK complex
KeywordsTelomere NHEJ BRCT domain SAP domain / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsEickhoff P / Fisher CEL / Inian O / Guettler S / Douglas ME
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Cancer Research UKC68409/A28129 United Kingdom
CitationJournal: Nature / Year: 2025
Title: Chromosome end protection by RAP1-mediated inhibition of DNA-PK.
Authors: Patrik Eickhoff / Ceylan Sonmez / Charlotte E L Fisher / Oviya Inian / Theodoros I Roumeliotis / Angela Dello Stritto / Jörg Mansfeld / Jyoti S Choudhary / Sebastian Guettler / Francisca ...Authors: Patrik Eickhoff / Ceylan Sonmez / Charlotte E L Fisher / Oviya Inian / Theodoros I Roumeliotis / Angela Dello Stritto / Jörg Mansfeld / Jyoti S Choudhary / Sebastian Guettler / Francisca Lottersberger / Max E Douglas /
Abstract: During classical non-homologous end joining (cNHEJ), DNA-dependent protein kinase (DNA-PK) encapsulates free DNA ends, forming a recruitment platform for downstream end-joining factors including ...During classical non-homologous end joining (cNHEJ), DNA-dependent protein kinase (DNA-PK) encapsulates free DNA ends, forming a recruitment platform for downstream end-joining factors including ligase 4 (LIG4). DNA-PK can also bind telomeres and regulate their resection, but does not initiate cNHEJ at this position. How the end-joining process is regulated in this context-specific manner is currently unclear. Here we show that the shelterin components TRF2 and RAP1 form a complex with DNA-PK that directly represses its end-joining function at telomeres. Biochemical experiments and cryo-electron microscopy reveal that when bound to TRF2, RAP1 establishes a network of interactions with KU and DNA that prevents DNA-PK from recruiting LIG4. In mouse and human cells, RAP1 is redundant with the Apollo nuclease in repressing cNHEJ at chromosome ends, demonstrating that the inhibition of DNA-PK prevents telomere fusions in parallel with overhang-dependent mechanisms. Our experiments show that the end-joining function of DNA-PK is directly and specifically repressed at telomeres, establishing a molecular mechanism for how individual linear chromosomes are maintained in mammalian cells.
History
DepositionDec 21, 2023-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19252.png

Downloads & links

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Map

FileDownload / File: emd_19252.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 384 pix.
= 360.96 Å		0.94 Å/pix.
x 384 pix.
= 360.96 Å		0.94 Å/pix.
x 384 pix.
= 360.96 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.43
Minimum - Maximum-1.7321444 - 3.2517211
Average (Standard dev.)0.00002208432 (±0.07364315)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 360.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_19252_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_19252_half_map_2.map
Projections & Slices
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Sample components

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Entire : Telomeric RAP1:DNA-PK complex

EntireName: Telomeric RAP1:DNA-PK complex
Components
  • Complex: Telomeric RAP1:DNA-PK complex

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Supramolecule #1: Telomeric RAP1:DNA-PK complex

SupramoleculeName: Telomeric RAP1:DNA-PK complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
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: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 370172
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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