9ZOB | pdb_00009zob

CryoEM structure of DNA-PK bound to N7 nucleosome, state 2

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history. 

Literature

DNA-PK driven nucleosome unwrapping enables NHEJ in chromatin

Lu, W., Vogt, A., Lees-Miller, S.P., He, Y.

(2026) Nat Commun 

Macromolecule Content 

  • Total Structure Weight: 812.71 kDa 
  • Atom Count: 50,123 
  • Modeled Residue Count: 5,795 
  • Deposited Residue Count: 6,627 
  • Unique protein chains: 8
  • Unique nucleic acid chains: 2

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-dependent protein kinase catalytic subunitA [auth M]4,128Homo sapiensMutation(s): 0 
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P78527 (Homo sapiens)
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PHAROS:  P78527
GTEx:  ENSG00000253729 
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Unknown peptideB [auth N]20Homo sapiensMutation(s): 0 
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 6C [auth K]609Homo sapiensMutation(s): 0 
EC: 5.6.2.4 (UniProt), 4.2.99.18 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P12956 (Homo sapiens)
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GTEx:  ENSG00000196419 
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA repair protein Ku80D [auth L]732Homo sapiensMutation(s): 0 
Gene Names: XRCC5, G22P2
EC: 4.2.99.18 (PDB Primary Data), 5.6.2.4 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P13010 (Homo sapiens)
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PHAROS:  P13010
GTEx:  ENSG00000079246 
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UniProt GroupP13010
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H3E [auth A],
N [auth E]		112Xenopus laevisMutation(s): 0 
Gene Names: LOC121398065, LOC108703785, LOC121398067
UniProt
Find proteins for A0A310TTQ1 (Xenopus laevis)
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H4F [auth B],
I [auth F]		87Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2AG [auth C],
J [auth G]		117Xenopus laevisMutation(s): 0 
Gene Names: LOC494591, h2ac14.L, hist1h2aj, hist1h2aj.L
UniProt
Find proteins for Q6AZJ8 (Xenopus laevis)
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2BH [auth D],
K [auth H]		99Xenopus laevisMutation(s): 0 
Gene Names: XELAEV_18032686mg
UniProt
Find proteins for A0A1L8FQ56 (Xenopus laevis)
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Reference Sequence
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Entity ID: 9
MoleculeChains LengthOrganismImage
DNA (154-MER)L [auth J]154Homo sapiens
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Reference Sequence
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Entity ID: 10
MoleculeChains LengthOrganismImage
DNA (154-MER)M [auth I]154Homo sapiens
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
UNK
Query on UNK		B [auth N]L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

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View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

  • Released Date: 2026-09-16 
    • Deposition Author(s): Lu, W., He, Y.
Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2026-09-16
    Type: Initial release