9NOD | pdb_00009nod

[4,3,12-2] Shifted tensegrity triangle with an (arm,center,arm) distribution of (4,3,12) base pairs and 2 nt sticky ends

• PDB DOI: https://doi.org/10.2210/pdb9NOD/pdb
• NAKB: 9NOD

• Classification: DNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2025-03-09 Released: 2025-09-10 
• Deposition Author(s): Horvath, A., Woloszyn, K., Vecchioni, S., Ohayon, Y.P., Sha, R.
• Funding Organization(s): Office of Naval Research (ONR), Department of Energy (DOE, United States), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 7.23 Å
• R-Value Free: 
  0.262 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.235 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Starting Model: experimental

Literature

Shifted tensegrity triangles

Horvath, A., Woloszyn, K., Vecchioni, S., Ohayon, Y.P., Sha, R.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 12.78 kDa 
• Atom Count: 851 
• Modeled Residue Count: 42 
• Deposited Residue Count: 42 
• Unique nucleic acid chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*AP*TP*TP*CP*TP*CP*TP*AP*CP*TP*GP*TP*GP*GP*AP*T)-3')	A	18	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*CP*AP*TP*CP*CP*T)-3')	B	7	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*GP*AP*CP*AP*GP*TP*AP*GP*AP*GP*AP*AP*T)-3')	C	14	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*CP*C)-3')	D	3	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 7.23 Å
• R-Value Free:  0.262 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.235 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.487	α = 90
b = 89.487	β = 90
c = 139.818	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-10 
Deposition Author(s): Horvath, A., Woloszyn, K., Vecchioni, S., Ohayon, Y.P., Sha, R.

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Funding Organization	Location	Grant Number
Office of Naval Research (ONR)	United States	N000141912596
Department of Energy (DOE, United States)	United States	DE-SC0007991
National Science Foundation (NSF, United States)	United States	CCF-2106790
National Science Foundation (NSF, United States)	United States	GCR-2317843

Revision History  

• Version 1.0: 2025-09-10
  Type: Initial release