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- PDB-9zmm: CryoEM structure of Ku heterodimer bound to N7 nucleosome -

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Basic information

Entry
Database: PDB / ID: 9zmm
TitleCryoEM structure of Ku heterodimer bound to N7 nucleosome
Components
  • (DNA (154-mer)) x 2
  • (X-ray repair cross-complementing protein ...) x 2
  • Histone H2A
  • Histone H2B
  • Histone H3
  • Histone H4
KeywordsDNA BINDING PROTEIN/DNA / Complex / DNA repair / NHEJ / Nucleosome / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


Ku70:Ku80 complex / negative regulation of t-circle formation / 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 / nonhomologous end joining complex / cellular response to X-ray / regulation of smooth muscle cell proliferation ...Ku70:Ku80 complex / negative regulation of t-circle formation / 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 / nonhomologous end joining complex / cellular response to X-ray / regulation of smooth muscle cell proliferation / double-strand break repair via classical nonhomologous end joining / Cytosolic sensors of pathogen-associated DNA / nuclear telomere cap complex / IRF3-mediated induction of type I IFN / cellular hyperosmotic salinity response / U3 snoRNA binding / regulation of telomere maintenance / recombinational repair / protein localization to chromosome, telomeric region / 2-LTR circle formation / telomeric repeat DNA binding / 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 / activation of innate immune response / telomere maintenance / cyclin binding / DNA-(apurinic or apyrimidinic site) lyase / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / site of DNA damage / double-strand break repair via nonhomologous end joining / small-subunit processome / Nonhomologous End-Joining (NHEJ) / cellular response to gamma radiation / protein-DNA complex / enzyme activator activity / nucleosomal DNA binding / innate immune response in mucosa / double-strand break repair / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / DNA recombination / antimicrobial humoral immune response mediated by antimicrobial peptide / double-stranded DNA binding / heterochromatin formation / scaffold protein binding / secretory granule lumen / transcription regulator complex / antibacterial humoral response / ficolin-1-rich granule lumen / innate immune response / damaged DNA binding / DNA helicase activity / chromosome, telomeric region / transcription cis-regulatory region binding / ribonucleoprotein complex / chromosome / protein heterodimerization activity / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / DNA damage response / nucleolus / Neutrophil degranulation / positive regulation of DNA-templated transcription / protein-containing complex binding / DNA-templated transcription / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / protein-containing complex / DNA binding / RNA binding / nucleoplasm / ATP binding / extracellular region / membrane / nucleus / cytosol
Similarity search - Function
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, 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 (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
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2B / Histone H3 / DNA repair protein Ku70 / DNA repair protein Ku80 / Histone H4
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.89 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 10, 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
I: DNA (154-mer)
J: DNA (154-mer)
E: Histone H3
F: Histone H4
G: Histone H2A
H: Histone H2B
A: Histone H3
B: Histone H4
C: Histone H2A
D: Histone H2B
K: X-ray repair cross-complementing protein 6
L: X-ray repair cross-complementing protein 5


Theoretical massNumber of molelcules
Total (without water)330,00012
Polymers330,00012
Non-polymers00
Water181
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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DNA chain , 2 types, 2 molecules IJ

#1: DNA chain DNA (154-mer)


Mass: 47768.418 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: 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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Protein , 4 types, 8 molecules EAFBGCHD

#3: Protein Histone H3


Mass: 11859.927 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
#4: 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) / Production host: Escherichia coli HB101 (bacteria) / References: UniProt: P62799
#5: Protein Histone H2A


Mass: 24946.154 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli HB101 (bacteria)
#6: Protein Histone H2B


Mass: 11179.959 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: XELAEV_18032686mg / Production host: Escherichia coli HB101 (bacteria) / References: UniProt: A0A1L8FQ56

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

#7: 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 / CTC75 / 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: 57998.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC6, G22P1 / Production host: Spodoptera frugiperda (fall armyworm)
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
#8: 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 / CTC85 / 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: 60972.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC5, G22P2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P13010, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement

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Non-polymers , 1 types, 1 molecules

#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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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

Component
IDNameTypeEntity IDParent-IDSource
1Complex of Ku bound to Nucleosome with 7bp overhangCOMPLEX#1-#80RECOMBINANT
2Nucleosome with 7bp overhangCOMPLEX#1-#61RECOMBINANT
3Ku70/80COMPLEX#7-#81RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.356 MDaNO
210.203 MDaYES
310.1525 MDaYES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Xenopus laevis (African clawed frog)8355
43Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Spodoptera frugiperda (fall armyworm)7108
32Escherichia coli HB101 (bacteria)634468
43Spodoptera frugiperda (fall armyworm)7108
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
IDNameVersionCategory
1cryoSPARCparticle selection
2Topazparticle selection
3PHENIX1.21.2_5419model refinement
14cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 81691 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 211.69 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004521776
ELECTRON MICROSCOPYf_angle_d0.700730701
ELECTRON MICROSCOPYf_chiral_restr0.04393465
ELECTRON MICROSCOPYf_plane_restr0.00572845
ELECTRON MICROSCOPYf_dihedral_angle_d27.59955346

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