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- PDB-8rd4: Telomeric RAP1:DNA-PK complex -

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Basic information

Entry
Database: PDB / ID: 8rd4
TitleTelomeric RAP1:DNA-PK complex
Components
  • (DNA (41-MER)) x 2
  • (X-ray repair cross-complementing protein ...) x 2
  • DNA-dependent protein kinase catalytic subunit
  • Telomeric repeat-binding factor 2-interacting protein 1
KeywordsDNA BINDING PROTEIN / Telomere NHEJ BRCT domain SAP domain
Function / homology
Function and homology information


negative regulation of DNA recombination at telomere / protection from non-homologous end joining at telomere / positive regulation of platelet formation / Ku70:Ku80 complex / negative regulation of telomere maintenance / negative regulation of t-circle formation / T cell receptor V(D)J recombination / DNA end binding / pro-B cell differentiation / shelterin complex ...negative regulation of DNA recombination at telomere / protection from non-homologous end joining at telomere / positive regulation of platelet formation / Ku70:Ku80 complex / negative regulation of telomere maintenance / negative regulation of t-circle formation / T cell receptor V(D)J recombination / DNA end binding / pro-B cell differentiation / shelterin complex / small-subunit processome assembly / positive regulation of lymphocyte differentiation / telomere maintenance via telomere lengthening / DNA-dependent protein kinase activity / Telomere C-strand synthesis initiation / DNA-dependent protein kinase complex / histone H2AXS139 kinase activity / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination / nonhomologous end joining complex / immature B cell differentiation / regulation of smooth muscle cell proliferation / cellular response to X-ray / Telomere C-strand (Lagging Strand) Synthesis / nuclear telomere cap complex / double-strand break repair via alternative nonhomologous end joining / G-rich strand telomeric DNA binding / regulation of epithelial cell proliferation / double-strand break repair via classical nonhomologous end joining / telomere capping / Cytosolic sensors of pathogen-associated DNA / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / IRF3-mediated induction of type I IFN / Removal of the Flap Intermediate from the C-strand / regulation of hematopoietic stem cell differentiation / positive regulation of neurogenesis / recombinational repair / regulation of telomere maintenance / protein localization to chromosome, telomeric region / U3 snoRNA binding / maturation of 5.8S rRNA / T cell lineage commitment / cellular hyperosmotic salinity response / regulation of double-strand break repair via homologous recombination / negative regulation of cGAS/STING signaling pathway / positive regulation of double-strand break repair via nonhomologous end joining / nuclear chromosome / 2-LTR circle formation / B cell lineage commitment / telomeric DNA binding / hematopoietic stem cell proliferation / negative regulation of protein phosphorylation / positive regulation of telomere maintenance / positive regulation of protein kinase activity / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / site of DNA damage / peptidyl-threonine phosphorylation / Telomere Extension By Telomerase / 5'-deoxyribose-5-phosphate lyase activity / hematopoietic stem cell differentiation / ectopic germ cell programmed cell death / ATP-dependent activity, acting on DNA / telomere maintenance via telomerase / somitogenesis / phosphatase binding / Packaging Of Telomere Ends / mitotic G1 DNA damage checkpoint signaling / neurogenesis / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere maintenance / activation of innate immune response / DNA helicase activity / Inhibition of DNA recombination at telomere / cyclin binding / Meiotic synapsis / positive regulation of erythrocyte differentiation / positive regulation of translation / cellular response to leukemia inhibitory factor / response to gamma radiation / male germ cell nucleus / small-subunit processome / Nonhomologous End-Joining (NHEJ) / enzyme activator activity / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to gamma radiation / positive regulation of NF-kappaB transcription factor activity / protein-DNA complex / regulation of circadian rhythm / brain development / peptidyl-serine phosphorylation / protein destabilization / protein modification process / double-strand break repair via nonhomologous end joining / DNA Damage/Telomere Stress Induced Senescence / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cellular response to insulin stimulus
Similarity search - Function
Rap1 Myb domain / Rap1 Myb domain / TRF2-interacting telomeric protein/Rap1, C-terminal / TRF2-interacting telomeric protein/Rap1, C-terminal domain superfamily / TRF2-interacting telomeric protein/Rap1 - C terminal domain / TE2IP/Rap1 / Ku70, bridge and pillars domain superfamily / : / DNA-dependent protein kinase catalytic subunit, CC3 / DNA-dependent protein kinase catalytic subunit, catalytic domain ...Rap1 Myb domain / Rap1 Myb domain / TRF2-interacting telomeric protein/Rap1, C-terminal / TRF2-interacting telomeric protein/Rap1, C-terminal domain superfamily / TRF2-interacting telomeric protein/Rap1 - C terminal domain / TE2IP/Rap1 / Ku70, bridge and pillars domain superfamily / : / DNA-dependent protein kinase catalytic subunit, CC3 / DNA-dependent protein kinase catalytic subunit, catalytic domain / DNA-dependent protein kinase catalytic subunit, CC5 / DNA-dependent protein kinase catalytic subunit, CC1/2 / DNA-PKcs, N-terminal / DNA-dependent protein kinase catalytic subunit, CC3 / DNA-PKcs, CC5 / DNA-PKcs, N-terminal / DNA-dependent protein kinase catalytic subunit, CC1/2 / NUC194 / Ku70 / Ku, C-terminal / Ku, C-terminal domain superfamily / Ku C terminal domain like / Ku80 / Ku70/Ku80 C-terminal arm / Ku70/Ku80 C-terminal arm / Ku70/Ku80, N-terminal alpha/beta / Ku70/Ku80 N-terminal alpha/beta domain / Ku70/Ku80 beta-barrel domain / Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen / Ku70/Ku80 beta-barrel domain / SPOC-like, C-terminal domain superfamily / SAP domain superfamily / BRCT domain / SAP motif profile. / SAP domain / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / : / FATC domain / PIK-related kinase, FAT / FAT domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / BRCT domain / BRCT domain superfamily / von Willebrand factor A-like domain superfamily / Homeobox-like domain superfamily / Armadillo-like helical / Armadillo-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / X-ray repair cross-complementing protein 6 / X-ray repair cross-complementing protein 5 / DNA-dependent protein kinase catalytic subunit / Telomeric repeat-binding factor 2-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.58 Å
AuthorsEickhoff, P. / Fisher, C.E.L. / Inian, O. / Guettler, S. / Douglas, M.E.
Funding support United Kingdom, 1items
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 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year / _em_admin.last_update
Revision 1.2Apr 30, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.3Jul 16, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-dependent protein kinase catalytic subunit
D: Telomeric repeat-binding factor 2-interacting protein 1
E: X-ray repair cross-complementing protein 6
F: X-ray repair cross-complementing protein 5
X: DNA (41-MER)
Y: DNA (41-MER)


Theoretical massNumber of molelcules
Total (without water)728,4396
Polymers728,4396
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area37060 Å2
ΔGint-238 kcal/mol
Surface area226120 Å2

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Components

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Protein , 2 types, 2 molecules AD

#1: Protein DNA-dependent protein kinase catalytic subunit / DNA-PK catalytic subunit / DNA-PKcs / DNPK1 / p460


Mass: 469673.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P78527, non-specific serine/threonine protein kinase
#2: Protein Telomeric repeat-binding factor 2-interacting protein 1


Mass: 44314.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TERF2IP / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NYB0

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X-ray repair cross-complementing protein ... , 2 types, 2 molecules EF

#3: Protein X-ray repair cross-complementing protein 6 / 5'-deoxyribose-5-phosphate lyase Ku70 / 5'-dRP lyase Ku70 / 70 kDa subunit of Ku antigen / ATP- ...5'-deoxyribose-5-phosphate lyase Ku70 / 5'-dRP lyase Ku70 / 70 kDa subunit of Ku antigen / ATP-dependent DNA helicase 2 subunit 1 / ATP-dependent DNA helicase II 70 kDa subunit / CTC box-binding factor 75 kDa subunit / CTCBF / DNA repair protein XRCC6 / Lupus Ku autoantigen protein p70 / Ku70 / Thyroid-lupus autoantigen / TLAA / X-ray repair complementing defective repair in Chinese hamster cells 6


Mass: 69945.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC6, G22P1 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P12956, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases
#4: Protein X-ray repair cross-complementing protein 5 / 86 kDa subunit of Ku antigen / ATP-dependent DNA helicase 2 subunit 2 / ATP-dependent DNA helicase ...86 kDa subunit of Ku antigen / ATP-dependent DNA helicase 2 subunit 2 / ATP-dependent DNA helicase II 80 kDa subunit / CTC box-binding factor 85 kDa subunit / CTCBF / DNA repair protein XRCC5 / Ku80 / Ku86 / Lupus Ku autoantigen protein p86 / Nuclear factor IV / Thyroid-lupus autoantigen / TLAA / X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining)


Mass: 82812.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC5, G22P2 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P13010, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement

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DNA chain , 2 types, 2 molecules XY

#5: DNA chain DNA (41-MER)


Mass: 31103.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (41-MER)


Mass: 30589.674 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Telomeric RAP1:DNA-PK complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.58 Å / Resolution method: OTHER / Num. of particles: 526885
Details: Composite map, resolution estimated from overall consensus map using a FSC 0.143 cut-off
Symmetry type: POINT

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