9Y3C | pdb_00009y3c

[21-7B nWC] 21 bp tensegrity triangle with one set of Watson-Crick sticky ends, one of non-Watson-Crick sticky ends, and one of blunt ends

• PDB DOI: https://doi.org/10.2210/pdb9Y3C/pdb
• NAKB: 9Y3C

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


• Deposited: 2025-09-02 Released: 2025-11-05 
• 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: 6.43 Å
• R-Value Free: 
  0.244 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Blunt-End 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 and generated by PISA (software)

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 38.62 kDa 
• Atom Count: 2,565 
• Modeled Residue Count: 126 
• Deposited Residue Count: 126 
• Unique nucleic acid chains: 7

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')	A	21	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*GP*TP*CP*TP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3')	B [auth E]	14	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*GP*TP*CP*AP*G)-3')	C [auth D]	15	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*TP*GP*AP*CP*CP*TP*GP*GP*CP*AP*GP*GP*AP*CP*GP*TP*AP*CP*T)-3')	D [auth B]	21	synthetic construct

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*TP*AP*CP*GP*TP*GP*GP*CP*TP*CP*G)-3')	E [auth F]	13	synthetic construct

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*AP*CP*GP*AP*GP*CP*CP*TP*GP*AP*TP*CP*GP*GP*AP*CP*AP*AP*GP*A)-3')	F [auth C]	21	synthetic construct

Entity ID: 7
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*CP*AP*CP*CP*GP*AP*TP*CP*AP*CP*CP*TP*GP*CP*CP*AP*CP*CP*GP*T)-3')	G [auth M]	21	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 6.43 Å
• R-Value Free:  0.244 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.139	α = 90
b = 125.139	β = 90
c = 187.813	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: 2025-11-05 
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: 2025-11-05
  Type: Initial release