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- PDB-8sjt: [3T14+10] Self-assembling left-handed tensegrity triangle with 14... -

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Basic information

Entry
Database: PDB / ID: 8sjt
Title[3T14+10] Self-assembling left-handed tensegrity triangle with 14 interjunction base pairs and a 10 bp linker with R3 symmetry
Components
  • DNA (5'-D(*AP*CP*CP*TP*CP*CP*TP*GP*AP*GP*GP*TP*CP*GP*AP*GP*C)-3')
  • DNA (5'-D(*GP*AP*CP*TP*CP*TP*GP*CP*TP*A)-3')
  • DNA (5'-D(*GP*TP*TP*AP*GP*CP*AP*GP*AP*G)-3')
  • DNA (5'-D(*TP*CP*GP*CP*TP*CP*AP*GP*CP*CP*TP*GP*AP*CP*TP*CP*A)-3')
  • DNA (5'-D(P*CP*AP*CP*GP*TP*GP*GP*AP*CP*AP*GP*GP*AP*G)-3')
  • DNA (5'-D(P*GP*TP*GP*AP*GP*TP*CP*TP*CP*CP*AP*CP*GP*T)-3')
KeywordsDNA / Tensegrity triangle / DNA nanotechnology / nanomaterials
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 9.38 Å
AuthorsJanowski, J. / Vecchioni, S. / Sha, R. / Ohayon, Y.P.
Funding support United States, France, 6items
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
National Aeronautic Space Administration (NASA, United States)2020 NASA Center Innovation Fund United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Engineering tertiary chirality in helical biopolymers.
Authors: Janowski, J. / Pham, V.A.B. / Vecchioni, S. / Woloszyn, K. / Lu, B. / Zou, Y. / Erkalo, B. / Perren, L. / Rueb, J. / Madnick, J. / Mao, C. / Saito, M. / Ohayon, Y.P. / Jonoska, N. / Sha, R.
History
DepositionApr 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,0676
Polymers25,0676
Non-polymers00
Water00
1
A: DNA (5'-D(P*CP*AP*CP*GP*TP*GP*GP*AP*CP*AP*GP*GP*AP*G)-3')
B: DNA (5'-D(*AP*CP*CP*TP*CP*CP*TP*GP*AP*GP*GP*TP*CP*GP*AP*GP*C)-3')
C: DNA (5'-D(*TP*CP*GP*CP*TP*CP*AP*GP*CP*CP*TP*GP*AP*CP*TP*CP*A)-3')
D: DNA (5'-D(P*GP*TP*GP*AP*GP*TP*CP*TP*CP*CP*AP*CP*GP*T)-3')
X: DNA (5'-D(*GP*AP*CP*TP*CP*TP*GP*CP*TP*A)-3')
Y: DNA (5'-D(*GP*TP*TP*AP*GP*CP*AP*GP*AP*G)-3')

A: DNA (5'-D(P*CP*AP*CP*GP*TP*GP*GP*AP*CP*AP*GP*GP*AP*G)-3')
B: DNA (5'-D(*AP*CP*CP*TP*CP*CP*TP*GP*AP*GP*GP*TP*CP*GP*AP*GP*C)-3')
C: DNA (5'-D(*TP*CP*GP*CP*TP*CP*AP*GP*CP*CP*TP*GP*AP*CP*TP*CP*A)-3')
D: DNA (5'-D(P*GP*TP*GP*AP*GP*TP*CP*TP*CP*CP*AP*CP*GP*T)-3')
X: DNA (5'-D(*GP*AP*CP*TP*CP*TP*GP*CP*TP*A)-3')
Y: DNA (5'-D(*GP*TP*TP*AP*GP*CP*AP*GP*AP*G)-3')

A: DNA (5'-D(P*CP*AP*CP*GP*TP*GP*GP*AP*CP*AP*GP*GP*AP*G)-3')
B: DNA (5'-D(*AP*CP*CP*TP*CP*CP*TP*GP*AP*GP*GP*TP*CP*GP*AP*GP*C)-3')
C: DNA (5'-D(*TP*CP*GP*CP*TP*CP*AP*GP*CP*CP*TP*GP*AP*CP*TP*CP*A)-3')
D: DNA (5'-D(P*GP*TP*GP*AP*GP*TP*CP*TP*CP*CP*AP*CP*GP*T)-3')
X: DNA (5'-D(*GP*AP*CP*TP*CP*TP*GP*CP*TP*A)-3')
Y: DNA (5'-D(*GP*TP*TP*AP*GP*CP*AP*GP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)75,20218
Polymers75,20218
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)212.243, 212.243, 164.272
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallH3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

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DNA chain , 6 types, 6 molecules ABCDXY

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


Mass: 4354.843 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*AP*CP*CP*TP*CP*CP*TP*GP*AP*GP*GP*TP*CP*GP*AP*GP*C)-3')


Mass: 5188.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*CP*GP*CP*TP*CP*AP*GP*CP*CP*TP*GP*AP*CP*TP*CP*A)-3')


Mass: 5123.324 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*GP*TP*GP*AP*GP*TP*CP*TP*CP*CP*AP*CP*GP*T)-3')


Mass: 4271.778 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain DNA (5'-D(*GP*AP*CP*TP*CP*TP*GP*CP*TP*A)-3')


Mass: 3019.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (5'-D(*GP*TP*TP*AP*GP*CP*AP*GP*AP*G)-3')


Mass: 3109.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 28.41 Å3/Da / Density % sol: 95.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 100 mM MOPS, 1.25 M magnesium sulfate / Temp details: 338K-293K at 0.4K/hr

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.00718 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Mar 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00718 Å / Relative weight: 1
ReflectionResolution: 9.38→80.205 Å / Num. obs: 1416 / % possible obs: 85.5 % / Redundancy: 10.1 % / Biso Wilson estimate: 1016.23 Å2 / CC1/2: 0.999 / Net I/σ(I): 7.3
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsCC1/2Diffraction-IDMean I/σ(I) obs% possible all
9.38-10.57110.22010.0381
19.137-80.2058.82030.999119.7100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5W6W

5w6w


Resolution: 9.38→48.66 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 45.938
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2029 75 5.41 %
Rwork0.1783 1311 -
obs0.1795 1386 76.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 1099.06 Å2
Refinement stepCycle: LAST / Resolution: 9.38→48.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1669 0 0 1669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811868
X-RAY DIFFRACTIONf_angle_d1.70642871
X-RAY DIFFRACTIONf_chiral_restr0.0723324
X-RAY DIFFRACTIONf_plane_restr0.008382
X-RAY DIFFRACTIONf_dihedral_angle_d38.1531798
LS refinement shellResolution: 9.38→48.66 Å
RfactorNum. reflection% reflection
Rfree0.2029 75 -
Rwork0.1783 1311 -
obs--76.66 %
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)
11.41889801538-1.5313081943-1.272409665952.113409734740.6851336221631.77469107960.6426709831340.85536514011-0.454652985059-1.02246749164-0.5988441157650.6737158608561.12925489683-1.784320445261.047527143448.767775869384.075943190153.633516398716.59311266075-4.9482019858511.9978978565-24.38311170739.3151502607851.4243415407
20.4573359749030.768320192894-0.4526121325110.35508523566-0.1099078358460.03129652489543.967505517911.48095028763-1.51025224016-1.451137854141.456153900270.3435764350061.807551108732.10513559040.2897265316438.31687555271-1.399394176411.318702725084.62940630058-5.174209422745.19832537207-38.67512919664.4989423322159.6203550512
30.9851884467250.3585963414150.4531872660440.1690088464610.1927695462390.1482447518462.362882959983.008334779092.617146934840.7466374719924.771383700461.78776861179-5.60759508792-2.322128918063.810245204719.0797349517-3.489158513313.416013874956.39332911411.55652201028.733953641-35.47616533950.52298286634669.2508717321
40.610414728374-0.892374790421-0.4618885326541.551950174570.8946238446770.6555041052622.48348712269-0.3993924297662.692517952971.556405838310.695700008438-0.6558672514760.064748310880.7958847292570.3624815152685.59034447453-4.89099179798-1.141363608515.887125388493.0262349209710.3251346813-16.89765832442.4961859547858.0708193047
50.05636267058710.0467719287696-0.05876548547750.2911769206320.03286225528130.04874172587550.5908123516740.09524504619290.3459099092011.434751787290.07665399883580.669585830226-0.837776476370.103472568242-0.24702182789.184031459260.604966081405-3.2739242850613.7761849438-1.4326393908812.8871397322-59.2958879894-11.684973870629.3996750105
60.202260797615-0.09354052395240.02656782039840.05874233434660.008847519599750.0126347496986-0.947690909620.0643731193542-0.3173447666580.150756973560.4890828003910.1384084989171.63224680585-0.68633768988-0.87771016446111.28344439932.1117253004-1.5991151924414.3117327521-0.46758429069516.0262967989-54.4723372286-8.6494586212732.2961384638
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 14)AA1 - 14
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 17)BB1 - 17
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 17)CC1 - 17
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 14)DD1 - 14
5X-RAY DIFFRACTION5(chain 'X' and resid 1 through 10)XE1 - 10
6X-RAY DIFFRACTION6(chain 'Y' and resid 1 through 10)YF1 - 10

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