[English] 日本語
Yorodumi
- PDB-7u3y: [L233] Self-assembling tensegrity triangle with two turns, three ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7u3y
Title[L233] Self-assembling tensegrity triangle with two turns, three turns and three turns of DNA per axis by linker addition with P1 symmetry
Components
  • DNA (5'-D(*AP*AP*CP*CP*TP*AP*CP*CP*TP*GP*GP*CP*AP*GP*GP*AP*CP*GP*AP*CP*T)-3')
  • DNA (5'-D(*AP*CP*TP*GP*AP*TP*GP*TP*GP*GP*TP*AP*GP*G)-3')
  • 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')
  • 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')
  • DNA (5'-D(*CP*TP*TP*AP*GP*CP*AP*TP*AP*G)-3')
  • DNA (5'-D(*GP*AP*TP*CP*TP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3')
  • DNA (5'-D(*TP*GP*CP*GP*CP*TP*AP*GP*CP*G)-3')
  • DNA (5'-D(*TP*TP*AP*GP*TP*CP*GP*TP*GP*GP*CP*TP*CP*G)-3')
  • DNA (5'-D(P*GP*TP*CP*TP*AP*TP*GP*CP*TP*A)-3')
  • DNA (5'-D(P*TP*CP*AP*CP*CP*TP*GP*CP*CP*AP*CP*CP*GP*TP*AP*CP*AP*CP*CP*GP*A)-3')
  • DNA (5'-D(P*TP*CP*CP*GP*CP*TP*AP*GP*CP*G)-3')
KeywordsDNA / Tensegrity triangle / self-assembling crystal
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.06 Å
AuthorsWoloszyn, K. / Vecchioni, S. / Seeman, N.C. / Sha, R. / Ohayon, Y.P.
Funding support United States, France, 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
Human Frontier Science Program (HFSP)RPG0010/2017 France
National Science Foundation (NSF, United States)DMR-1420073 United States
CitationJournal: Adv Mater / Year: 2022
Title: Augmented DNA Nanoarchitectures: A Structural Library of 3D Self-Assembling Tensegrity Triangle Variants.
Authors: Woloszyn, K. / Vecchioni, S. / Ohayon, Y.P. / Lu, B. / Ma, Y. / Huang, Q. / Zhu, E. / Chernovolenko, D. / Markus, T. / Jonoska, N. / Mao, C. / Seeman, N.C. / Sha, R.
History
DepositionFeb 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
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(*CP*AP*CP*GP*AP*GP*CP*CP*TP*GP*AP*TP*CP*GP*GP*AP*CP*AP*AP*GP*A)-3')
E: DNA (5'-D(*TP*TP*AP*GP*TP*CP*GP*TP*GP*GP*CP*TP*CP*G)-3')
D: DNA (5'-D(*GP*AP*TP*CP*TP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3')
B: 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')
F: DNA (5'-D(*AP*CP*TP*GP*AP*TP*GP*TP*GP*GP*TP*AP*GP*G)-3')
C: DNA (5'-D(*AP*AP*CP*CP*TP*AP*CP*CP*TP*GP*GP*CP*AP*GP*GP*AP*CP*GP*AP*CP*T)-3')
M: DNA (5'-D(P*TP*CP*AP*CP*CP*TP*GP*CP*CP*AP*CP*CP*GP*TP*AP*CP*AP*CP*CP*GP*A)-3')
U: DNA (5'-D(P*TP*CP*CP*GP*CP*TP*AP*GP*CP*G)-3')
V: DNA (5'-D(*TP*GP*CP*GP*CP*TP*AP*GP*CP*G)-3')
X: DNA (5'-D(P*GP*TP*CP*TP*AP*TP*GP*CP*TP*A)-3')
Y: DNA (5'-D(*CP*TP*TP*AP*GP*CP*AP*TP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)50,79611
Polymers50,79611
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.140, 99.588, 100.157
Angle α, β, γ (deg.)104.297, 103.013, 98.105
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

-
DNA chain , 11 types, 11 molecules AEDBFCMUVXY

#1: DNA chain 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')


Mass: 6466.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*TP*TP*AP*GP*TP*CP*GP*TP*GP*GP*CP*TP*CP*G)-3')


Mass: 4302.788 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*AP*TP*CP*TP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3')


Mass: 4302.788 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain 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')


Mass: 6457.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain DNA (5'-D(*AP*CP*TP*GP*AP*TP*GP*TP*GP*GP*TP*AP*GP*G)-3')


Mass: 4375.851 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (5'-D(*AP*AP*CP*CP*TP*AP*CP*CP*TP*GP*GP*CP*AP*GP*GP*AP*CP*GP*AP*CP*T)-3')


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


Mass: 6313.090 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#8: DNA chain DNA (5'-D(P*TP*CP*CP*GP*CP*TP*AP*GP*CP*G)-3')


Mass: 3020.979 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#9: DNA chain DNA (5'-D(*TP*GP*CP*GP*CP*TP*AP*GP*CP*G)-3')


Mass: 3061.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#10: DNA chain DNA (5'-D(P*GP*TP*CP*TP*AP*TP*GP*CP*TP*A)-3')


Mass: 3035.003 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#11: DNA chain DNA (5'-D(*CP*TP*TP*AP*GP*CP*AP*TP*AP*G)-3')


Mass: 3044.016 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: MOPS, Magnesium sulfate, Sodium hydroxide / Temp details: 338-293 at 0.4/hr, 293-277 at 0.1/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: Sep 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00743 Å / Relative weight: 1
ReflectionResolution: 5.93→94.388 Å / Num. obs: 3645 / % possible obs: 85 % / Redundancy: 3.6 % / Biso Wilson estimate: 414.28 Å2 / CC1/2: 1 / Net I/σ(I): 7.9
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsCC1/2Diffraction-ID
5.93-6.7693.72030.0141
18.337-94.3883.62030.9991

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GBI

3gbi


Resolution: 6.06→37.92 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.1385
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1375 182 5.12 %
Rwork0.0906 3374 -
obs0.0927 3556 61.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 628.4 Å2
Refinement stepCycle: LAST / Resolution: 6.06→37.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3379 0 0 3379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0183783
X-RAY DIFFRACTIONf_angle_d1.70935817
X-RAY DIFFRACTIONf_chiral_restr0.0943656
X-RAY DIFFRACTIONf_plane_restr0.0081166
X-RAY DIFFRACTIONf_dihedral_angle_d42.79851619
LS refinement shellResolution: 6.06→37.92 Å
RfactorNum. reflection% reflection
Rfree0.1375 182 -
Rwork0.0906 3374 -
obs--61.26 %
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)
14.43650839799-3.816966067740.4511689656896.07126101169-6.199844374327.46666834398-4.15108579944-3.80024187694-2.10310844732-3.749227598427.9829277701-4.9225638668-0.839224811862-1.79180631606-3.897129411175.14824387224-0.404979448309-0.9047179476175.53050753324-1.159123592737.6362630314116.37996776093.93511761962-5.41413553714
28.618435811725.491731843234.279139526877.098272294725.276696116414.939171885446.37510698792.10932477852-2.498049600091.234942359331.20719699392-3.037177677280.6346717197841.34555589926-6.221963220635.877295047430.6681106984141.745332070645.54696215759-0.5768135840156.9858324610523.6457877882-9.805993843554.41210911044
32.051538654552.45871739101-2.131150559963.59391046656-2.446220432882.11024213332.484249072310.6534504793493.811506811580.137883465811.83404679234-2.6598525259-5.532365092680.4793660302923.8682429781810.17976508650.3117056303553.557850487773.59676350834-0.33586155085110.33061882665.0450198048725.748210778-6.98971211694
43.68968453441-4.119439341780.3306463734148.28237247927-0.8195259104470.05741515328292.300486372990.265285558659-1.10200625850.495398366563-1.23611202656-0.812146039035-8.02740163705-5.83433352675-1.827185376629.0991644890.0459192336142-0.4778352810177.99977221883-0.08321417053153.16992646605-6.3371584702915.59043524133.86652100533
52.05611747993-3.569012465822.914769972026.62071230791-5.283920993423.64801372481-2.48018530187-5.4989703805-3.164115106075.637075448281.719873276581.15933611074-5.84718670585-0.5840610729340.7547407845475.34669171058-1.42735724267-0.72350888799411.1960938061-0.01746141046484.61138524287-12.31591617530.63452963671423.5064757495
67.19249932671-1.91416380631-0.6133589396038.7193102138-7.281432305322.87546040654-2.15751935217-2.1243538152-9.202343456190.1931464517412.10432444707-0.545882364378-0.544814271226-2.23725203893-0.7003062728033.17025778409-0.0738830201156-1.784282017777.00328747372-0.7858877359156.816763933560.926175698404-7.5330672819714.5462805375
78.17628097565-1.564534353913.414185352930.474775636365-0.7213724052851.299018251134.99902433402-5.21025829627-2.3685025184-4.670943748233.20470243397-4.40003634006-5.9060174388-1.41657970042-1.420850750097.78095998154-0.09891625828211.163060840586.61358933036-0.7476728108984.516038053094.331829196524.357222067364.88768733777
82.087437944163.99408565036-2.016031934257.37705033774-3.930889532731.90487615962-1.340541281422.29996765291-2.87262836286-1.67911893541-2.21539937009-3.79639647763-1.34652466415-2.986860984953.4871663459611.49615062260.9659141855510.1445283766594.253870187810.06874607813828.5276382823429.4836999117-45.7725250875-4.82164257907
98.45011675817-2.785579955630.8314358317011.18575449227-1.634608104986.12709032333-0.392213357606-0.629810355112-0.277556217072.76951438338-1.960124324613.143832725681.72062814241-0.1333606516971.790861336477.820118854220.241917380907-0.7540124157564.78788085904-1.2910655855310.748916439727.7379563427-40.0575418495-5.23750480773
100.814443968274-0.4834162704490.01570556115320.516339061741-0.2648644723410.491217722493-0.9900794855691.54100902916-0.991125725571-2.110409801710.8828850967590.306379082712-0.3861929710240.55862530738-0.71230985757116.02918977013.722176753783.450770531578.32360336262.698020143266.174205774973.2155027543633.1226119917-42.0322233121
110.854241548612-1.81862536089-1.561558056758.442273418061.16441310814.26662989346-3.88547757389-0.02896960086472.34835347474-2.417118169491.24385056724-1.342984378621.098873807090.921695539831.976498077918.13112348387-0.0812783896419-1.4410469948411.96877477470.06404132974253.511661809711.747053751730.9957361228-36.825545106
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 101 through 121)AA101 - 121
2X-RAY DIFFRACTION2(chain 'E' and resid 101 through 114)EB101 - 114
3X-RAY DIFFRACTION3(chain 'D' and resid 101 through 114)DC101 - 114
4X-RAY DIFFRACTION4(chain 'B' and resid 101 through 121)BD101 - 121
5X-RAY DIFFRACTION5(chain 'F' and resid 101 through 114)FE101 - 114
6X-RAY DIFFRACTION6(chain 'C' and resid 101 through 121)CF101 - 121
7X-RAY DIFFRACTION7(chain 'M' and resid 101 through 121)MG101 - 121
8X-RAY DIFFRACTION8(chain 'U' and resid 112 through 121)UH112 - 121
9X-RAY DIFFRACTION9(chain 'V' and resid 101 through 110)VI101 - 110
10X-RAY DIFFRACTION10(chain 'X' and resid 112 through 121)XJ112 - 121
11X-RAY DIFFRACTION11(chain 'Y' and resid 101 through 110)YK101 - 110

+
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