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- PDB-8sjr: [3T17] Self-assembling right-handed tensegrity triangle with 17 i... -

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Basic information

Entry
Database: PDB / ID: 8sjr
Title[3T17] Self-assembling right-handed tensegrity triangle with 17 interjunction base pairs and R3 symmetry
Components
  • DNA (5'-D(*CP*AP*GP*CP*AP*GP*CP*CP*TP*GP*AP*AP*TP*AP*CP*CP*GP*CP*A)-3')
  • DNA (5'-D(*TP*GP*CP*GP*CP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3')
  • DNA (5'-D(P*GP*CP*GP*GP*TP*AP*TP*TP*CP*AP*CP*CP*AP*CP*GP*AP*T)-3')
  • DNA (5'-D(P*TP*CP*GP*TP*GP*GP*AP*CP*AP*GP*CP*G)-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: 5.25 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(*CP*AP*GP*CP*AP*GP*CP*CP*TP*GP*AP*AP*TP*AP*CP*CP*GP*CP*A)-3')
B: DNA (5'-D(P*GP*CP*GP*GP*TP*AP*TP*TP*CP*AP*CP*CP*AP*CP*GP*AP*T)-3')
C: DNA (5'-D(*TP*GP*CP*GP*CP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(P*TP*CP*GP*TP*GP*GP*AP*CP*AP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)18,9784
Polymers18,9784
Non-polymers00
Water00
1
A: DNA (5'-D(*CP*AP*GP*CP*AP*GP*CP*CP*TP*GP*AP*AP*TP*AP*CP*CP*GP*CP*A)-3')
B: DNA (5'-D(P*GP*CP*GP*GP*TP*AP*TP*TP*CP*AP*CP*CP*AP*CP*GP*AP*T)-3')
C: DNA (5'-D(*TP*GP*CP*GP*CP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(P*TP*CP*GP*TP*GP*GP*AP*CP*AP*GP*CP*G)-3')

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

A: DNA (5'-D(*CP*AP*GP*CP*AP*GP*CP*CP*TP*GP*AP*AP*TP*AP*CP*CP*GP*CP*A)-3')
B: DNA (5'-D(P*GP*CP*GP*GP*TP*AP*TP*TP*CP*AP*CP*CP*AP*CP*GP*AP*T)-3')
C: DNA (5'-D(*TP*GP*CP*GP*CP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(P*TP*CP*GP*TP*GP*GP*AP*CP*AP*GP*CP*G)-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)170.214, 170.214, 80.252
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(*CP*AP*GP*CP*AP*GP*CP*CP*TP*GP*AP*AP*TP*AP*CP*CP*GP*CP*A)-3')


Mass: 5783.765 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*GP*CP*GP*GP*TP*AP*TP*TP*CP*AP*CP*CP*AP*CP*GP*AP*T)-3')


Mass: 5187.374 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*GP*CP*GP*CP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3')


Mass: 4303.775 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*TP*CP*GP*TP*GP*GP*AP*CP*AP*GP*CP*G)-3')


Mass: 3703.416 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: 11.79 Å3/Da / Density % sol: 89.57 %
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: Mar 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00744 Å / Relative weight: 1
ReflectionResolution: 5.25→85.107 Å / Num. obs: 3630 / % possible obs: 81 % / Redundancy: 9.7 % / Biso Wilson estimate: 412.28 Å2 / CC1/2: 0.903 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsMean I/σ(I) obsCC1/2% possible all
5.253-6.07910.96.166205
13.159-85.1079.220615.10.886100

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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: 5.25→38.72 Å / SU ML: -0 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 48.7139
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2501 206 5.67 %
Rwork0.2095 3424 -
obs0.2117 3630 55.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 407.89 Å2
Refinement stepCycle: LAST / Resolution: 5.25→38.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1265 0 0 1265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00861416
X-RAY DIFFRACTIONf_angle_d1.04532177
X-RAY DIFFRACTIONf_chiral_restr0.0557246
X-RAY DIFFRACTIONf_plane_restr0.005762
X-RAY DIFFRACTIONf_dihedral_angle_d40.8242606
LS refinement shellResolution: 5.25→38.72 Å
RfactorNum. reflection% reflection
Rfree0.2501 206 -
Rwork0.2095 3424 -
obs--55.9 %
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)
10.798032319121-0.275206723787-0.3402482151075.61386118947-5.18236514115.240895721541.669235822160.710358221738-1.43594139367-0.993439500130.263876393267-0.1057445347052.42939904151-0.7865314022480.5348234136171.81855130798-2.75738119072-0.4683996832525.40513669511-4.951414294954.9882590989531.5248078349-8.60392272998-5.27635851254
22.934548219480.8392715164310.7191542818827.13677517523-2.176046144637.304286725312.142180521010.5618078312142.875845293790.3198981967911.6591158176-1.15568292281-1.31805273104-2.56964442879-0.9834422393341.37401784446-0.0297706237650.5886478985145.76596709051-3.233009807456.5174578774821.9411249791-2.16464341435-11.1659682998
35.977521977063.031923348281.407710822458.167363990782.246628164434.201299171194.78369826621-0.753477965116-1.57470865651-0.0335012898556-0.9947999582-1.588942906291.16569901695-1.01150281161-1.707198237371.63322330021.47703853856-0.7838753934593.266170843971.144099778146.4006966908742.9427768041-0.397087865178-12.9601437825
40.53333429524-0.5678338957110.2758070902640.8768885480.5298254067572.090004633311.253124466610.531878061842-0.2759845737120.1046319797380.3814686695170.905573840246-1.540874304970.00760286132833.103825249752.90149524033-0.08699055613293.231954014523.5621431407-2.414602101976.4431611163632.75416887165.97304489318-17.9677280563
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 101 through 119)AA101 - 119
2X-RAY DIFFRACTION2(chain 'B' and resid 98 through 114)BB98 - 114
3X-RAY DIFFRACTION3(chain 'C' and resid 101 through 114)CC101 - 114
4X-RAY DIFFRACTION4(chain 'D' and resid 110 through 121)DD110 - 121

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