8WOH | pdb_00008woh

human dsDNA sensor CCDC25 complexed with 18bp DNA

• PDB DOI: https://doi.org/10.2210/pdb8WOH/pdb
• NAKB: 8WOH

• Classification: DNA BINDING PROTEIN
• Organism(s): synthetic construct, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-10-07 Released: 2024-10-09 
• Deposition Author(s): Wen, Y., Wu, B.X.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.291 (Depositor), 0.286 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: in silico

Literature

human dsDNA sensor CCDC25 complexed with 18bp DNA

Wen, Y., Wu, B.X.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 57.59 kDa 
• Atom Count: 3,686 
• Modeled Residue Count: 400 
• Deposited Residue Count: 426 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Coiled-coil domain-containing protein 25	C [auth B], D [auth A]	194	Homo sapiens	Mutation(s): 0  Gene Names: CCDC25
UniProt & NIH Common Fund Data Resources
Find proteins for Q86WR0 (Homo sapiens) Explore Q86WR0  Go to UniProtKB:  Q86WR0
PHAROS:  Q86WR0 GTEx:  ENSG00000147419

Entity ID: 1
Molecule	Chains	Length	Organism	Image
18bp DNA	A [auth C]	19	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
18bp DNA	B [auth D]	19	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.291 (Depositor), 0.286 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.66	α = 90
b = 77.964	β = 90
c = 99.378	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-09 
Deposition Author(s): Wen, Y., Wu, B.X.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-10-09
  Type: Initial release