[English] 日本語
Yorodumi
- PDB-8cym: [2T7+9bp Linker] Self-Assembled 3D DNA Hexagonal Tensegrity Trian... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8cym
Title[2T7+9bp Linker] Self-Assembled 3D DNA Hexagonal Tensegrity Triangle with 9 bp Sticky-End Linker
Components
  • DNA (5'-D(*AP*CP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*C)-3')
  • DNA (5'-D(*GP*AP*TP*GP*CP*GP*AP*GP*T)-3')
  • DNA (5'-D(*GP*TP*AP*CP*TP*CP*GP*CP*A)-3')
  • DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')
  • DNA (5'-D(P*CP*CP*GP*TP*AP*CP*A)-3')
  • DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
KeywordsDNA / Tensegrity triangle / synthetic construct / self-assembly
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7.76 Å
AuthorsLu, B. / Vecchioni, S. / Ohayon, Y.P. / Seeman, N.C. / Mao, C. / Sha, R.
Funding support United States, 7items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CTS1120890 United States
National Science Foundation (NSF, United States)CCF-1117210 United States
National Science Foundation (NSF, United States)EFRI-1332411 United States
National Science Foundation (NSF, United States)CHE-1708776 United States
Office of Naval Research (ONR)N000141110729 United States
Office of Naval Research (ONR)N000140911118 United States
Department of Energy (DOE, United States)DESC0007991 United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Programmable 3D Hexagonal Geometry of DNA Tensegrity Triangles.
Authors: Lu, B. / Woloszyn, K. / Ohayon, Y.P. / Yang, B. / Zhang, C. / Mao, C. / Seeman, N.C. / Vecchioni, S. / Sha, R.
History
DepositionMay 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,2696
Polymers18,2696
Non-polymers00
Water00
1
A: DNA (5'-D(*AP*CP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*C)-3')
B: DNA (5'-D(P*CP*CP*GP*TP*AP*CP*A)-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')
I: DNA (5'-D(*GP*AP*TP*GP*CP*GP*AP*GP*T)-3')
J: DNA (5'-D(*GP*TP*AP*CP*TP*CP*GP*CP*A)-3')

A: DNA (5'-D(*AP*CP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*C)-3')
B: DNA (5'-D(P*CP*CP*GP*TP*AP*CP*A)-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')
I: DNA (5'-D(*GP*AP*TP*GP*CP*GP*AP*GP*T)-3')
J: DNA (5'-D(*GP*TP*AP*CP*TP*CP*GP*CP*A)-3')

A: DNA (5'-D(*AP*CP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*C)-3')
B: DNA (5'-D(P*CP*CP*GP*TP*AP*CP*A)-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')
I: DNA (5'-D(*GP*AP*TP*GP*CP*GP*AP*GP*T)-3')
J: DNA (5'-D(*GP*TP*AP*CP*TP*CP*GP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)54,80718
Polymers54,80718
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Unit cell
Length a, b, c (Å)173.130, 173.130, 87.833
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

-
DNA chain , 6 types, 6 molecules ABCDIJ

#1: DNA chain DNA (5'-D(*AP*CP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*C)-3')


Mass: 6417.164 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*CP*CP*GP*TP*AP*CP*A)-3')


Mass: 2082.400 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)
#5: DNA chain DNA (5'-D(*GP*AP*TP*GP*CP*GP*AP*GP*T)-3')


Mass: 2795.847 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (5'-D(*GP*TP*AP*CP*TP*CP*GP*CP*A)-3')


Mass: 2715.799 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 21.16 Å3/Da / Density % sol: 94.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.75 M ammonium sulfate, 120 mM Tris, 120 mM Acetic Acid, 6 mM EDTA
Temp details: 338-293 at 0.4/hr

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.00743 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00743 Å / Relative weight: 1
ReflectionResolution: 7.76→86.57 Å / Num. obs: 1347 / % possible obs: 87 % / Redundancy: 9.8 % / Biso Wilson estimate: 186.16 Å2 / CC1/2: 1 / Net I/σ(I): 5.1
Reflection shellResolution: 7.76→8.84 Å / Num. unique obs: 191 / CC1/2: 0.389

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7R96

7r96


Resolution: 7.76→49.98 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.2463
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.113 63 4.72 %
Rwork0.0794 1271 -
obs0.0808 1334 73.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 635.74 Å2
Refinement stepCycle: LAST / Resolution: 7.76→49.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1218 0 0 1218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00891361
X-RAY DIFFRACTIONf_angle_d1.00082086
X-RAY DIFFRACTIONf_chiral_restr0.0591236
X-RAY DIFFRACTIONf_plane_restr0.006260
X-RAY DIFFRACTIONf_dihedral_angle_d39.4779575
LS refinement shellResolution: 7.76→49.98 Å
RfactorNum. reflection% reflection
Rfree0.113 63 -
Rwork0.0794 1271 -
obs--73.7 %

+
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