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- PDB-9zp9: CryoEM structure of DNA-PK bound to N7 nucleosome, state 1 -

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Basic information

Entry
Database: PDB / ID: 9zp9
TitleCryoEM structure of DNA-PK bound to N7 nucleosome, state 1
Components
  • (DNA (154-MER)) x 2
  • (X-ray repair cross-complementing protein ...) x 2
  • DNA-dependent protein kinase catalytic subunit
  • Histone H2A
  • Histone H2B
  • Histone H3
  • Histone H4
  • Unknown peptide
KeywordsDNA BINDING PROTEIN / nhej / dna repair / DNA-PK / nucleosome
Function / homology
Function and homology information


positive regulation of platelet formation / 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 / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination ...positive regulation of platelet formation / 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 / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination / histone H2AXS139 kinase activity / nonhomologous end joining complex / double-stranded telomeric DNA binding / 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 / cellular hyperosmotic salinity response / U3 snoRNA binding / recombinational repair / maturation of 5.8S rRNA / protein localization to chromosome, telomeric region / positive regulation of double-strand break repair via nonhomologous end joining / negative regulation of cGAS/STING signaling pathway / 2-LTR circle formation / peptidyl-threonine phosphorylation / telomeric repeat DNA binding / negative regulation of protein phosphorylation / DNA 3'-5' helicase / 5'-deoxyribose-5-phosphate lyase activity / ATP-dependent activity, acting on DNA / 3'-5' DNA helicase activity / telomere maintenance via telomerase / mitotic G1 DNA damage checkpoint signaling / positive regulation of erythrocyte differentiation / activation of innate immune response / telomere maintenance / cyclin binding / protein modification process / DNA-(apurinic or apyrimidinic site) lyase / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA helicase activity / site of DNA damage / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of translation / small-subunit processome / Nonhomologous End-Joining (NHEJ) / cellular response to gamma radiation / protein-DNA complex / peptidyl-serine phosphorylation / double-strand break repair via nonhomologous end joining / regulation of circadian rhythm / nucleosomal DNA binding / innate immune response in mucosa / double-strand break repair / structural constituent of chromatin / cellular response to insulin stimulus / nucleosome / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / transcription regulator complex / chromatin organization / DNA recombination / antimicrobial humoral immune response mediated by antimicrobial peptide / double-stranded DNA binding / heterochromatin formation / scaffold protein binding / secretory granule lumen / antibacterial humoral response / ficolin-1-rich granule lumen / damaged DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / protein kinase activity / innate immune response / protein phosphorylation / chromosome, telomeric region / non-specific serine/threonine protein kinase / transcription cis-regulatory region binding / protein heterodimerization activity / protein domain specific binding / protein serine kinase activity / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / protein serine/threonine kinase activity / DNA damage response / negative regulation of apoptotic process / nucleolus / Neutrophil degranulation / positive regulation of DNA-templated transcription / chromatin / protein-containing complex binding / enzyme binding / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity
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 / : / 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 / von Willebrand factor A-like domain superfamily / : / Histone H2B signature. / Histone H2B / Histone H2B / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Armadillo-like helical / Armadillo-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H3 / Histone H2B / : / DNA repair protein Ku80 / DNA repair protein Ku70 / DNA-dependent protein kinase catalytic subunit / Histone H4
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.88 Å
AuthorsLu, W. / He, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2026
Title: DNA-PK driven nucleosome unwrapping enables NHEJ in chromatin
Authors: Lu, W. / Vogt, A. / Lees-Miller, S.P. / He, Y.
History
DepositionDec 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 16, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone H3
B: Histone H4
C: Histone H2A
D: Histone H2B
E: Histone H3
F: Histone H4
G: Histone H2A
H: Histone H2B
I: DNA (154-MER)
J: DNA (154-MER)
K: X-ray repair cross-complementing protein 6
L: X-ray repair cross-complementing protein 5
M: DNA-dependent protein kinase catalytic subunit
N: Unknown peptide


Theoretical massNumber of molelcules
Total (without water)810,81814
Polymers810,81814
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 5 types, 9 molecules AEBFCGDHM

#1: Protein Histone H3


Mass: 12830.009 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC121398065, LOC108703785, LOC121398067 / Production host: Escherichia coli HB101 (bacteria) / References: UniProt: A0A310TTQ1
#2: Protein Histone H4


Mass: 9990.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: His4, H4 / Production host: Escherichia coli HB101 (bacteria) / References: UniProt: P84048
#3: Protein Histone H2A


Mass: 12183.232 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: XELAEV_18026403mg / Production host: Escherichia coli HB101 (bacteria) / References: UniProt: A0A974HJ06
#4: Protein Histone H2B


Mass: 10792.419 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC108704302 / Production host: Escherichia coli HB101 (bacteria) / References: UniProt: A0A8J1LZU9
#9: Protein DNA-dependent protein kinase catalytic subunit


Mass: 469673.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P78527

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (154-MER)


Mass: 47768.418 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#6: DNA chain DNA (154-MER)


Mass: 47306.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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

#7: Protein X-ray repair cross-complementing protein 6


Mass: 69945.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P12956
#8: Protein X-ray repair cross-complementing protein 5


Mass: 82812.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC5 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: G3R763, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement

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Protein/peptide , 1 types, 1 molecules N

#10: Protein/peptide Unknown peptide


Mass: 1720.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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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: DNA-PK bound to N7 ncp / Type: COMPLEX / Entity ID: #1-#6, #9-#10, #7-#8 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 220128 / Symmetry type: POINT

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