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- PDB-8sjo: [3T14] Self-assembling left-handed tensegrity triangle with 14 in... -

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Basic information

Entry
Database: PDB / ID: 8sjo
Title[3T14] Self-assembling left-handed tensegrity triangle with 14 interjunction base pairs and R3 symmetry
Components
  • DNA (5'-D(P*CP*AP*CP*GP*TP*GP*GP*AP*CP*AP*GP*GP*AP*G)-3')
  • DNA (5'-D(P*CP*AP*GP*CP*TP*CP*AP*GP*CP*CP*TP*GP*AP*CP*TP*CP*A)-3')
  • DNA (5'-D(P*GP*TP*GP*AP*GP*TP*CP*TP*CP*CP*AP*CP*GP*T)-3')
  • DNA (5'-D(P*TP*GP*CP*TP*CP*CP*TP*GP*AP*GP*GP*TP*CP*GP*AP*GP*C)-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: 7.08 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(P*TP*GP*CP*TP*CP*CP*TP*GP*AP*GP*GP*TP*CP*GP*AP*GP*C)-3')
C: DNA (5'-D(P*CP*AP*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')


Theoretical massNumber of molelcules
Total (without water)18,9784
Polymers18,9784
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(P*TP*GP*CP*TP*CP*CP*TP*GP*AP*GP*GP*TP*CP*GP*AP*GP*C)-3')
C: DNA (5'-D(P*CP*AP*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')

A: DNA (5'-D(P*CP*AP*CP*GP*TP*GP*GP*AP*CP*AP*GP*GP*AP*G)-3')
B: DNA (5'-D(P*TP*GP*CP*TP*CP*CP*TP*GP*AP*GP*GP*TP*CP*GP*AP*GP*C)-3')
C: DNA (5'-D(P*CP*AP*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')

A: DNA (5'-D(P*CP*AP*CP*GP*TP*GP*GP*AP*CP*AP*GP*GP*AP*G)-3')
B: DNA (5'-D(P*TP*GP*CP*TP*CP*CP*TP*GP*AP*GP*GP*TP*CP*GP*AP*GP*C)-3')
C: DNA (5'-D(P*CP*AP*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')


Theoretical massNumber of molelcules
Total (without water)56,93512
Polymers56,93512
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)166.834, 166.834, 107.618
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

#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(P*TP*GP*CP*TP*CP*CP*TP*GP*AP*GP*GP*TP*CP*GP*AP*GP*C)-3')


Mass: 5219.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*CP*AP*GP*CP*TP*CP*AP*GP*CP*CP*TP*GP*AP*CP*TP*CP*A)-3')


Mass: 5132.338 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)

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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: 15.19 Å3/Da / Density % sol: 91.9 %
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: 1.00744 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00744 Å / Relative weight: 1
ReflectionResolution: 6.951→86.307 Å / Num. obs: 1234 / % possible obs: 82.7 % / Redundancy: 10.7 % / Biso Wilson estimate: 723.22 Å2 / CC1/2: 0.998 / Net I/σ(I): 5.8
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsCC1/2Diffraction-IDMean I/σ(I) obs% possible all
6.951-8.14310.72080.0191
14.354-86.30710.42040.998116.499.5

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5W6W

5w6w


Resolution: 7.08→43.15 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 34.9744
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1314 31 2.79 %
Rwork0.1036 1082 -
obs0.1048 1113 65.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 1021.16 Å2
Refinement stepCycle: LAST / Resolution: 7.08→43.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1271 0 0 1271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061422
X-RAY DIFFRACTIONf_angle_d1.72522185
X-RAY DIFFRACTIONf_chiral_restr0.053248
X-RAY DIFFRACTIONf_plane_restr0.005362
X-RAY DIFFRACTIONf_dihedral_angle_d36.6367608
LS refinement shellResolution: 7.08→43.15 Å
RfactorNum. reflection% reflection
Rfree0.1314 31 -
Rwork0.1036 1082 -
obs--65.13 %
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)
10.055222105325-0.0211457699826-0.1175497568990.188367491844-0.02681455640550.139850333522-0.656637403577-0.2647927791710.37274411970.381041138038-0.64113936637-0.1789288267850.9997059890950.9982051413590.32038676032311.5959028499-1.75335059331-2.5253929784413.783882896-1.2493586832910.2319459585.2926196679726.32985319192.75212660281
20.137567486681-0.0320322900194-0.0575683219498-0.04303380630970.0312847878270.0147972284176-0.354938054225-1.4848567903-1.03889207671-0.939419464627-0.189814355179-0.05494752307560.6160177511120.00775792961908-0.27299420324511.2109667399-1.62831365668-0.87418099587213.1464573187-1.6003435122512.29180553118.280370598834.85808698281.0127875948
30.3955407522280.09109962842160.6322371738310.066807188649-0.05920599937060.913759223029-0.759835286573-2.66407688510.736147837218-0.5686996421741.2019441474-0.814740919595-0.3592575478460.981521340523-0.6872703987614.4105942665-0.805716388329-2.977403770428.751382436515.2949958486813.308349546718.615264679135.7167482296-15.5508043274
40.2273754096031.017493307570.3687346880025.689930566720.07197830287021.79834094250.11234162247-2.118262507313.158472827730.1149669249420.365397672459-0.7558875525951.02840710481.10655856939-1.0654066464910.3478154143-1.27927861438-1.1384403352312.2076635063-0.9189726650539.536559222366.7341745382316.6255662212-3.67645515516
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 16)AA1 - 14
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 13)BB1 - 13
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 15)CC1 - 15
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 17)DD1 - 14

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