9GYF | pdb_00009gyf

Ku70/80 with PAXX peptide mutation K193R

• PDB DOI: https://doi.org/10.2210/pdb9GYF/pdb
• EM Map EMD-51697: EMDB EMDataResource
• NAKB: 9GYF

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2024-10-02 Released: 2025-10-15 
• Deposition Author(s): Chaplin, A.K., Malewicz, M.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom), The Lister Institute of Preventive Medicine

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Ku70/80 with PAXX peptide mutation K193R

Chaplin, A.K., Malewicz, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 164.75 kDa 
• Atom Count: 8,717 
• Modeled Residue Count: 1,086 
• Deposited Residue Count: 1,395 
• Unique protein chains: 3
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
X-ray repair cross-complementing protein 6	A	609	Homo sapiens	Mutation(s): 0  Gene Names: XRCC6, G22P1 EC: 3.6.4 (PDB Primary Data), 4.2.99 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P12956 (Homo sapiens) Explore P12956  Go to UniProtKB:  P12956
PHAROS:  P12956 GTEx:  ENSG00000196419

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
X-ray repair cross-complementing protein 5	B	732	Homo sapiens	Mutation(s): 0  Gene Names: XRCC5, G22P2 EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for P13010 (Homo sapiens) Explore P13010  Go to UniProtKB:  P13010
PHAROS:  P13010 GTEx:  ENSG00000079246

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein PAXX	C	23	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BUH6 (Homo sapiens) Explore Q9BUH6  Go to UniProtKB:  Q9BUH6
GTEx:  ENSG00000148362

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA1	D	15	Homo sapiens

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA2	E	16	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4 (Subject of Investigation/LOI)	F [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-15 
Deposition Author(s): Chaplin, A.K., Malewicz, M.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/X00029X/1
The Lister Institute of Preventive Medicine	United Kingdom	--

Revision History  

• Version 1.0: 2025-10-15
  Type: Initial release