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- PDB-8sjs: [3T18] Self-assembling right-handed tensegrity triangle with 18 i... -

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Basic information

Entry
Database: PDB / ID: 8sjs
Title[3T18] Self-assembling right-handed tensegrity triangle with 18 interjunction base pairs and P63 symmetry
Components
  • DNA (5'-D(*CP*AP*GP*AP*GP*CP*CP*TP*GP*AP*CP*AP*TP*AP*CP*CP*GP*CP*A)-3')
  • DNA (5'-D(*TP*GP*CP*GP*CP*TP*GP*TP*GP*GP*CP*TP*C)-3')
  • DNA (5'-D(P*TP*CP*GP*TP*GP*GP*AP*CP*AP*GP*CP*G)-3')
  • DNA (5'-D(P*TP*GP*CP*GP*GP*TP*AP*TP*GP*TP*CP*AP*CP*CP*AP*CP*GP*A)-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: 6.31 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*AP*GP*CP*CP*TP*GP*AP*CP*AP*TP*AP*CP*CP*GP*CP*A)-3')
B: DNA (5'-D(P*TP*GP*CP*GP*GP*TP*AP*TP*GP*TP*CP*AP*CP*CP*AP*CP*GP*A)-3')
C: DNA (5'-D(*TP*GP*CP*GP*CP*TP*GP*TP*GP*GP*CP*TP*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*AP*GP*CP*CP*TP*GP*AP*CP*AP*TP*AP*CP*CP*GP*CP*A)-3')
B: DNA (5'-D(P*TP*GP*CP*GP*GP*TP*AP*TP*GP*TP*CP*AP*CP*CP*AP*CP*GP*A)-3')
C: DNA (5'-D(*TP*GP*CP*GP*CP*TP*GP*TP*GP*GP*CP*TP*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*AP*GP*CP*CP*TP*GP*AP*CP*AP*TP*AP*CP*CP*GP*CP*A)-3')
B: DNA (5'-D(P*TP*GP*CP*GP*GP*TP*AP*TP*GP*TP*CP*AP*CP*CP*AP*CP*GP*A)-3')
C: DNA (5'-D(*TP*GP*CP*GP*CP*TP*GP*TP*GP*GP*CP*TP*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*AP*GP*CP*CP*TP*GP*AP*CP*AP*TP*AP*CP*CP*GP*CP*A)-3')
B: DNA (5'-D(P*TP*GP*CP*GP*GP*TP*AP*TP*GP*TP*CP*AP*CP*CP*AP*CP*GP*A)-3')
C: DNA (5'-D(*TP*GP*CP*GP*CP*TP*GP*TP*GP*GP*CP*TP*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_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Unit cell
Length a, b, c (Å)194.203, 194.203, 55.434
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

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Components

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


Mass: 5516.579 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*C)-3')


Mass: 3974.570 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: 15.9 Å3/Da / Density % sol: 92.26 %
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 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Oct 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 6.307→97.102 Å / Num. obs: 2039 / % possible obs: 86.1 % / Redundancy: 19.4 % / Biso Wilson estimate: 413.95 Å2 / CC1/2: 1 / Net I/σ(I): 12.6
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID
6.307-7.0182070.3051
15.535-97.1022040.9991

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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: 6.31→41.78 Å / SU ML: 0.106 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.2512
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1191 99 4.93 %
Rwork0.1097 1909 -
obs0.1102 2008 73.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 547.85 Å2
Refinement stepCycle: LAST / Resolution: 6.31→41.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1265 0 0 1265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01681416
X-RAY DIFFRACTIONf_angle_d1.49212177
X-RAY DIFFRACTIONf_chiral_restr0.0963246
X-RAY DIFFRACTIONf_plane_restr0.00962
X-RAY DIFFRACTIONf_dihedral_angle_d41.1149606
LS refinement shellResolution: 6.31→41.78 Å
RfactorNum. reflection% reflection
Rfree0.1191 99 -
Rwork0.1097 1909 -
obs--73.77 %
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)
12.837937994913.574532593640.5448595305566.976406890262.127840630670.638621477947-3.732310173843.921779982230.179835190031-0.05005707070829.47533154561-3.36798589748-0.625841346986-1.11715444447-0.6935460521355.11354604328-0.797393744284-3.377083679215.750358571090.6682539085287.66500041222-86.73951300726.0903458634.61633103861
26.24812854709-1.996302153783.135437224111.108135795321.007174087999.65316144181-2.54278319228-0.409715094073-0.1873083428022.678739051752.902873354387.16379557348-3.733642842631.036412877080.3983448033734.632559159831.719026736250.3015624247043.9767431249-0.2865593656886.61212989993-93.419345860934.39745912759.21196563025
38.17570252081-4.824122508527.074091727367.73763664747-3.203616485236.53916829501-2.0462814846-1.193890129632.085800088313.744372820911.58308405944-4.580658549430.945562696112-4.56161512148-0.4134461723735.9003644298-1.16894409644-0.1593280668794.0483935175-0.01406344396353.94594680552-98.471482561811.776615126512.7339562021
40.694550211843-0.252316892971-2.245920939360.07346670473720.7363947627337.04383342993-3.00589359369-0.6228898621344.93860446191.312510560172.53809336575-0.338838644782-0.180523416374-0.196954394549-3.758974472883.563684696780.678008669768-2.236866706484.704698234570.2411677211549.8161829146-105.3256685120.821782162516.5930171593
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 101 through 118)BB101 - 118
3X-RAY DIFFRACTION3(chain 'C' and resid 101 through 113)CC101 - 113
4X-RAY DIFFRACTION4(chain 'D' and resid 101 through 112)DD101 - 112

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