9ZP9 | pdb_00009zp9

CryoEM structure of DNA-PK bound to N7 nucleosome, state 1

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.88 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: 810.82 kDa 
  • Atom Count: 50,103 
  • Modeled Residue Count: 5,794 
  • Deposited Residue Count: 6,609 
  • Unique protein chains: 8
  • Unique nucleic acid chains: 2

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H3
A, E
112Xenopus laevisMutation(s): 0 
Gene Names: LOC121398065, LOC108703785, LOC121398067
UniProt
Find proteins for A0A310TTQ1 (Xenopus laevis)
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UniProt GroupA0A310TTQ1
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H4
B, F
87Xenopus laevisMutation(s): 0 
Gene Names: His4, H4
UniProt
Find proteins for P84048 (Acrolepiopsis assectella)
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UniProt GroupP84048
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2A
C, G
111Xenopus laevisMutation(s): 0 
Gene Names: XELAEV_18026403mg
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2B
D, H
96Xenopus laevisMutation(s): 0 
Gene Names: LOC108704302
UniProt
Find proteins for A0A8J1LZU9 (Xenopus laevis)
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UniProt GroupA0A8J1LZU9
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 6609Homo 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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PHAROS:  P12956
GTEx:  ENSG00000196419 
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UniProt GroupP12956
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
X-ray repair cross-complementing protein 5732Homo sapiensMutation(s): 0 
Gene Names: XRCC5
EC: 3.6.4 (PDB Primary Data), 5.6.2.4 (UniProt), 4.2.99.18 (UniProt)
UniProt
Find proteins for G3R763 (Gorilla gorilla gorilla)
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-dependent protein kinase catalytic subunit4,128Homo 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: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Unknown peptide20Homo sapiensMutation(s): 0 
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Reference Sequence
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (154-MER)154Homo sapiens
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Reference Sequence
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (154-MER)154Homo sapiens
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Reference Sequence

Small Molecules

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

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.88 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