[English] 日本語
Yorodumi
- PDB-9c6u: [d2d3] Tensegrity triangle with deazapurine center and helical st... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9c6u
Title[d2d3] Tensegrity triangle with deazapurine center and helical strands (strands 2+3) with P63 symmetry
Components
  • DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
  • DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')
  • DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
  • DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
KeywordsDNA / self-assembling / tensegrity triangle / deaza
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5 Å
AuthorsVecchioni, S. / Sha, R. / Ohayon, Y. / Galindo, M. / Lopez-Chamorro, C. / Jong, M. / Woloszyn, K.
Funding support United States, 5items
OrganizationGrant numberCountry
Office of Naval Research (ONR)N000141912596 United States
Department of Energy (DOE, United States)DE-SC0007991 United States
National Science Foundation (NSF, United States)2106790 United States
National Science Foundation (NSF, United States)CCF-2106790 United States
National Science Foundation (NSF, United States)GCR-2317843 United States
CitationJournal: To Be Published
Title: Deazapurine DNA Nanostructures
Authors: Vecchioni, S.
History
DepositionJun 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)12,7854
Polymers12,7854
Non-polymers00
Water00
1
A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)38,35412
Polymers38,35412
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
2
A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')

A: DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')
B: DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)524,167164
Polymers524,167164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation1_445x-1,y-1,z1
crystal symmetry operation1_454x-1,y,z-11
crystal symmetry operation1_444x-1,y-1,z-11
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation2_454-y-1,x-y,z-11
crystal symmetry operation2_465-y-1,x-y+1,z1
crystal symmetry operation2_453-y-1,x-y,z-21
crystal symmetry operation2_464-y-1,x-y+1,z-11
crystal symmetry operation2_564-y,x-y+1,z-11
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_455-x+y-1,-x,z1
crystal symmetry operation3_345-x+y-2,-x-1,z1
crystal symmetry operation3_355-x+y-2,-x,z1
crystal symmetry operation3_344-x+y-2,-x-1,z-11
crystal symmetry operation3_354-x+y-2,-x,z-11
crystal symmetry operation3_454-x+y-1,-x,z-11
crystal symmetry operation4_354-x-2,-y,z-1/21
crystal symmetry operation4_454-x-1,-y,z-1/21
crystal symmetry operation4_464-x-1,-y+1,z-1/21
crystal symmetry operation4_353-x-2,-y,z-3/21
crystal symmetry operation4_453-x-1,-y,z-3/21
crystal symmetry operation4_463-x-1,-y+1,z-3/21
crystal symmetry operation4_455-x-1,-y,z+1/21
crystal symmetry operation4_465-x-1,-y+1,z+1/21
crystal symmetry operation5_344y-2,-x+y-1,z-1/21
crystal symmetry operation5_445y-1,-x+y-1,z+1/21
crystal symmetry operation5_454y-1,-x+y,z-1/21
crystal symmetry operation5_343y-2,-x+y-1,z-3/21
crystal symmetry operation5_444y-1,-x+y-1,z-1/21
crystal symmetry operation5_453y-1,-x+y,z-3/21
crystal symmetry operation5_455y-1,-x+y,z+1/21
crystal symmetry operation6_454x-y-1,x,z-1/21
crystal symmetry operation6_555x-y,x,z+1/21
crystal symmetry operation6_565x-y,x+1,z+1/21
crystal symmetry operation6_453x-y-1,x,z-3/21
crystal symmetry operation6_554x-y,x,z-1/21
crystal symmetry operation6_564x-y,x+1,z-1/21
crystal symmetry operation6_563x-y,x+1,z-3/21
Unit cell
Length a, b, c (Å)125.393, 125.393, 59.368
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

-
Components

#1: DNA chain DNA (5'-D(*(7GU)P*(7DA)P*(7GU)P*CP*(7DA)P*(7GU)P*CP*CP*TP*(7GU)P*TP*(7DA)P*CP*(7GU)P*(7GU)P*(7DA)P*CP*(7DA)P*TP*CP*(7DA))-3')


Mass: 6447.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*CP*CP*(7GU)P*TP*(7DA)P*CP*(7DA))-3')


Mass: 2079.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')


Mass: 1825.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')


Mass: 2432.614 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 100 mM MOPS, 1.25 M magnesium sulfate / Temp details: 338-293 at 0.4 degree/hr

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 2, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 5→33.76 Å / Num. obs: 1895 / % possible obs: 89.1 % / Redundancy: 10.3 % / Biso Wilson estimate: 196.61 Å2 / CC1/2: 0.994 / Net I/σ(I): 4.4
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID
5-5.4951.92110.7091
11.377-33.7617.92100.9921

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 5→33.76 Å / SU ML: 0.5403 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.2986
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2946 92 4.86 %
Rwork0.2475 1800 -
obs0.2499 1892 79.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 275.65 Å2
Refinement stepCycle: LAST / Resolution: 5→33.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 855 0 0 855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051948
X-RAY DIFFRACTIONf_angle_d1.01361435
X-RAY DIFFRACTIONf_chiral_restr0.05153
X-RAY DIFFRACTIONf_plane_restr0.00442
X-RAY DIFFRACTIONf_dihedral_angle_d38.1808330
LS refinement shellResolution: 5→33.76 Å
RfactorNum. reflection% reflection
Rfree0.2946 92 -
Rwork0.2475 1800 -
obs--79.06 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.52451895908-0.484646085056-3.47749051451.268549946110.1058496645848.784550573480.0977561893340.692638120756-1.28644227692-0.4773555365221.09439436988-0.3282240603040.122375894826-2.302675443912.260850906432.143527512080.7620001601315.930636159912.50628586144-0.07297932112623.39775839882-62.524-1.383-18.703
24.412895248343.09627759061.398402376026.055950080651.849318308860.6339733211220.412129013381-0.853757308838-0.7056392932110.1528101349560.541970045432-1.008573700920.1079455915732.71951697422-1.526689756163.24838268710.242265979746-2.592450037083.19675985827-1.914441241450.454083075252-46.33938.727-7.79
36.17187936708-5.85335129953-1.52821278147.899943276774.587396958975.15218498941.434196436720.9246294508126.16044232498-0.130026466633.89105854597-2.17264219527-0.82084820676-1.61269296834-2.908001499542.55395784266-0.1503886645120.3613298778742.207826496090.7481300876993.04202744003-55.34912.019-19.223
42.086111136910.0552143888642-2.550071742032.120566853912.898356339533.628596048732.763618892233.90955304232-0.9550360620895.97009392645-1.221690218224.007285891883.174778997866.189907493670.1694369886992.909548978330.3756924391380.259179353693.087222135070.007667104690722.64217262336-41.02547.0765.779
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 101:120 OR RESID 121:121 ) )A101 - 120
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 101:120 OR RESID 121:121 ) )A121
3X-RAY DIFFRACTION2( CHAIN B AND ( RESID 119:124 OR RESID 125:125 ) )B119 - 124
4X-RAY DIFFRACTION2( CHAIN B AND ( RESID 119:124 OR RESID 125:125 ) )B125
5X-RAY DIFFRACTION3( CHAIN C AND RESID 209:214 )C209 - 214
6X-RAY DIFFRACTION4( CHAIN D AND RESID 201:208 )D201 - 208

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more