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- PDB-7k19: CryoEM structure of DNA-PK catalytic subunit complexed with DNA (... -

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Basic information

Entry
Database: PDB / ID: 7k19
TitleCryoEM structure of DNA-PK catalytic subunit complexed with DNA (Complex I)
Components
  • DNA (5'-D(*AP*AP*GP*CP*AP*GP*TP*AP*GP*AP*GP*CP*AP*TP*GP*C)-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
KeywordsDNA BINDING PROTEIN/DNA / NHEJ / V(D)J recombination / DNA repair / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


positive regulation of platelet formation / T cell receptor V(D)J recombination / pro-B cell differentiation / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / immature B cell differentiation ...positive regulation of platelet formation / T cell receptor V(D)J recombination / pro-B cell differentiation / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / immature B cell differentiation / nonhomologous end joining complex / immunoglobulin V(D)J recombination / regulation of smooth muscle cell proliferation / Cytosolic sensors of pathogen-associated DNA / double-strand break repair via alternative nonhomologous end joining / IRF3-mediated induction of type I IFN / telomere capping / regulation of epithelial cell proliferation / regulation of hematopoietic stem cell differentiation / U3 snoRNA binding / T cell lineage commitment / maturation of 5.8S rRNA / negative regulation of cGAS/STING signaling pathway / B cell lineage commitment / positive regulation of double-strand break repair via nonhomologous end joining / ectopic germ cell programmed cell death / somitogenesis / mitotic G1 DNA damage checkpoint signaling / activation of innate immune response / telomere maintenance / positive regulation of erythrocyte differentiation / negative regulation of protein phosphorylation / protein-DNA complex / small-subunit processome / positive regulation of translation / response to gamma radiation / Nonhomologous End-Joining (NHEJ) / peptidyl-threonine phosphorylation / protein destabilization / brain development / protein modification process / regulation of circadian rhythm / double-strand break repair via nonhomologous end joining / cellular response to insulin stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / rhythmic process / double-strand break repair / E3 ubiquitin ligases ubiquitinate target proteins / heart development / T cell differentiation in thymus / double-stranded DNA binding / peptidyl-serine phosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / chromosome, telomeric region / non-specific serine/threonine protein kinase / protein kinase activity / positive regulation of apoptotic process / protein phosphorylation / protein domain specific binding / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / chromatin / negative regulation of apoptotic process / nucleolus / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / nucleoplasm / ATP binding / membrane / nucleus / cytosol
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 / : / 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 / Armadillo-like helical / Armadillo-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA-dependent protein kinase catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 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 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2021Provider: 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

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Structure visualization

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Assembly

Deposited unit
A: DNA-dependent protein kinase catalytic subunit
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')
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*AP*TP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)489,2534
Polymers489,2534
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: 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)
#3: DNA chain DNA (5'-D(*AP*AP*GP*CP*AP*GP*TP*AP*GP*AP*GP*CP*AP*TP*GP*C)-3')


Mass: 4956.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: complex I / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
21synthetic construct (others)32630
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
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 62117 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00629837
ELECTRON MICROSCOPYf_angle_d1.09540568
ELECTRON MICROSCOPYf_dihedral_angle_d18.15617987
ELECTRON MICROSCOPYf_chiral_restr0.0584665
ELECTRON MICROSCOPYf_plane_restr0.014994

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