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- PDB-7k0y: Cryo-EM structure of activated-form DNA-PK (complex VI) -

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Entry
Database: PDB / ID: 7k0y
TitleCryo-EM structure of activated-form DNA-PK (complex VI)
Components
  • DNA (5'-D(*AP*AP*GP*CP*AP*GP*TP*AP*GP*AP*GP*CP*A)-3')
  • DNA (5'-D(*GP*CP*AP*TP*GP*CP*TP*CP*TP*AP*CP*TP*GP*CP*TP*TP*CP*GP*AP*TP*AP*TP*CP*G)-3')
  • DNA-dependent protein kinase catalytic subunit
  • X-ray repair cross-complementing protein 5
  • X-ray repair cross-complementing protein 6
KeywordsDNA BINDING PROTEIN/DNA / DNA-dependent Protein Kinase / DNA repair / NHEJ / V(D)J recombination / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


positive regulation of platelet formation / DNA-dependent protein kinase complex / Ku70:Ku80 complex / negative regulation of t-circle formation / DNA-dependent protein kinase activity / DNA end binding / small-subunit processome assembly / positive regulation of lymphocyte differentiation / histone H2AXS139 kinase activity / DNA-dependent protein kinase-DNA ligase 4 complex ...positive regulation of platelet formation / DNA-dependent protein kinase complex / Ku70:Ku80 complex / negative regulation of t-circle formation / DNA-dependent protein kinase activity / DNA end binding / small-subunit processome assembly / positive regulation of lymphocyte differentiation / histone H2AXS139 kinase activity / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination / nonhomologous end joining complex / cellular response to X-ray / regulation of epithelial cell proliferation / regulation of smooth muscle cell proliferation / double-strand break repair via classical nonhomologous end joining / double-strand break repair via alternative nonhomologous end joining / Cytosolic sensors of pathogen-associated DNA / nuclear telomere cap complex / telomere capping / IRF3-mediated induction of type I IFN / regulation of hematopoietic stem cell differentiation / U3 snoRNA binding / regulation of telomere maintenance / recombinational repair / cellular hyperosmotic salinity response / protein localization to chromosome, telomeric region / maturation of 5.8S rRNA / positive regulation of double-strand break repair via nonhomologous end joining / 2-LTR circle formation / negative regulation of cGAS/STING signaling pathway / peptidyl-threonine phosphorylation / telomeric repeat DNA binding / negative regulation of protein phosphorylation / DNA 3'-5' helicase / 5'-deoxyribose-5-phosphate lyase activity / 3'-5' DNA helicase activity / ATP-dependent activity, acting on DNA / telomere maintenance via telomerase / mitotic G1 DNA damage checkpoint signaling / site of DNA damage / positive regulation of erythrocyte differentiation / activation of innate immune response / telomere maintenance / cyclin binding / DNA helicase activity / protein modification process / DNA-(apurinic or apyrimidinic site) lyase / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / positive regulation of translation / peptidyl-serine phosphorylation / small-subunit processome / Nonhomologous End-Joining (NHEJ) / cellular response to gamma radiation / protein-DNA complex / intrinsic apoptotic signaling pathway in response to DNA damage / regulation of circadian rhythm / double-strand break repair via nonhomologous end joining / cellular response to insulin stimulus / enzyme activator activity / rhythmic process / double-strand break repair / E3 ubiquitin ligases ubiquitinate target proteins / transcription regulator complex / scaffold protein binding / double-stranded DNA binding / DNA recombination / secretory granule lumen / ficolin-1-rich granule lumen / damaged DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / protein phosphorylation / protein kinase activity / chromosome, telomeric region / non-specific serine/threonine protein kinase / transcription cis-regulatory region binding / ribonucleoprotein complex / protein domain specific binding / innate immune response / protein serine kinase activity / negative regulation of DNA-templated transcription / protein serine/threonine kinase activity / ubiquitin protein ligase binding / Neutrophil degranulation / DNA damage response / nucleolus / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / chromatin / protein-containing complex binding / enzyme binding / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / protein-containing complex / DNA-templated transcription / DNA binding / RNA binding / extracellular region / nucleoplasm / ATP binding
Similarity search - Function
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 ...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, bridge and pillars domain superfamily / : / 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 / SAP motif profile. / SAP domain / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / von Willebrand factor, type A domain / : / FATC domain / PIK-related kinase, FAT / FAT domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / 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 / von Willebrand factor A-like domain superfamily / Alpha Horseshoe / Armadillo-like helical / Armadillo-type fold / Protein kinase-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA repair protein Ku70 / DNA repair protein Ku80 / DNA-dependent protein kinase catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsChen, X. / Gellert, M. / Yang, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: Mol Cell / Year: 2021
Title: Structure of an activated DNA-PK and its implications for NHEJ.
Authors: Xuemin Chen / Xiang Xu / Yun Chen / Joyce C Cheung / Huaibin Wang / Jiansen Jiang / Natalia de Val / Tara Fox / Martin Gellert / Wei Yang /
Abstract: DNA-dependent protein kinase (DNA-PK), like all phosphatidylinositol 3-kinase-related kinases (PIKKs), is composed of conserved FAT and kinase domains (FATKINs) along with solenoid structures made of ...DNA-dependent protein kinase (DNA-PK), like all phosphatidylinositol 3-kinase-related kinases (PIKKs), is composed of conserved FAT and kinase domains (FATKINs) along with solenoid structures made of HEAT repeats. These kinases are activated in response to cellular stress signals, but the mechanisms governing activation and regulation remain unresolved. For DNA-PK, all existing structures represent inactive states with resolution limited to 4.3 Å at best. Here, we report the cryoelectron microscopy (cryo-EM) structures of DNA-PKcs (DNA-PK catalytic subunit) bound to a DNA end or complexed with Ku70/80 and DNA in both inactive and activated forms at resolutions of 3.7 Å overall and 3.2 Å for FATKINs. These structures reveal the sequential transition of DNA-PK from inactive to activated forms. Most notably, activation of the kinase involves previously unknown stretching and twisting within individual solenoid segments and loosens DNA-end binding. This unprecedented structural plasticity of helical repeats may be a general regulatory mechanism of HEAT-repeat proteins.
History
DepositionSep 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2021Provider: repository / Type: Initial release
Revision 1.0Jan 6, 2021Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 6, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 6, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jan 6, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 6, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jan 6, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 6, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jan 6, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 6, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Jun 4, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 4, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

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Assembly

Deposited unit
A: DNA-dependent protein kinase catalytic subunit
B: X-ray repair cross-complementing protein 6
C: X-ray repair cross-complementing protein 5
D: DNA (5'-D(*GP*CP*AP*TP*GP*CP*TP*CP*TP*AP*CP*TP*GP*CP*TP*TP*CP*GP*AP*TP*AP*TP*CP*G)-3')
E: DNA (5'-D(*AP*AP*GP*CP*AP*GP*TP*AP*GP*AP*GP*CP*A)-3')
F: DNA (5'-D(*GP*CP*AP*TP*GP*CP*TP*CP*TP*AP*CP*TP*GP*CP*TP*TP*CP*GP*AP*TP*AP*TP*CP*G)-3')
G: DNA (5'-D(*AP*AP*GP*CP*AP*GP*TP*AP*GP*AP*GP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)646,9677
Polymers646,9677
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein DNA-dependent protein kinase 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 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: Homo sapiens (human)
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
#3: 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: Homo sapiens (human)
References: UniProt: P13010, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#4: DNA chain DNA (5'-D(*GP*CP*AP*TP*GP*CP*TP*CP*TP*AP*CP*TP*GP*CP*TP*TP*CP*GP*AP*TP*AP*TP*CP*G)-3')


Mass: 7311.714 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain DNA (5'-D(*AP*AP*GP*CP*AP*GP*TP*AP*GP*AP*GP*CP*A)-3')


Mass: 4956.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
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: DNA-PK / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
21synthetic construct (others)32630
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 254646 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00940791
ELECTRON MICROSCOPYf_angle_d1.17555431
ELECTRON MICROSCOPYf_dihedral_angle_d17.86424654
ELECTRON MICROSCOPYf_chiral_restr0.0646293
ELECTRON MICROSCOPYf_plane_restr0.0126832

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