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- PDB-7arv: TwistTower_native-twist -

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Basic information

Entry
Database: PDB / ID: 7arv
TitleTwistTower_native-twist
Components
  • (STAPLE STRAND) x 194
  • SCAFFOLD STRAND
KeywordsDNA / DNA Origami
Function / homologyDNA / DNA (> 10) / DNA (> 100) / DNA (> 1000)
Function and homology information
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.4 Å
AuthorsKube, M. / Kohler, F. / Feigl, E. / Nagel-Yuksel, B. / Willner, E.M. / Funke, J.J. / Gerling, T. / Stommer, P. / Honemann, M.N. / Martin, T.G. ...Kube, M. / Kohler, F. / Feigl, E. / Nagel-Yuksel, B. / Willner, E.M. / Funke, J.J. / Gerling, T. / Stommer, P. / Honemann, M.N. / Martin, T.G. / Scheres, S.H.W. / Dietz, H.
Funding support Germany, European Union, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
European Research Council (ERC)European Union
Max Planck Society Germany
CitationJournal: Nat Commun / Year: 2020
Title: Revealing the structures of megadalton-scale DNA complexes with nucleotide resolution.
Authors: Massimo Kube / Fabian Kohler / Elija Feigl / Baki Nagel-Yüksel / Elena M Willner / Jonas J Funke / Thomas Gerling / Pierre Stömmer / Maximilian N Honemann / Thomas G Martin / Sjors H W ...Authors: Massimo Kube / Fabian Kohler / Elija Feigl / Baki Nagel-Yüksel / Elena M Willner / Jonas J Funke / Thomas Gerling / Pierre Stömmer / Maximilian N Honemann / Thomas G Martin / Sjors H W Scheres / Hendrik Dietz /
Abstract: The methods of DNA nanotechnology enable the rational design of custom shapes that self-assemble in solution from sets of DNA molecules. DNA origami, in which a long template DNA single strand is ...The methods of DNA nanotechnology enable the rational design of custom shapes that self-assemble in solution from sets of DNA molecules. DNA origami, in which a long template DNA single strand is folded by many short DNA oligonucleotides, can be employed to make objects comprising hundreds of unique DNA strands and thousands of base pairs, thus in principle providing many degrees of freedom for modelling complex objects of defined 3D shapes and sizes. Here, we address the problem of accurate structural validation of DNA objects in solution with cryo-EM based methodologies. By taking into account structural fluctuations, we can determine structures with improved detail compared to previous work. To interpret the experimental cryo-EM maps, we present molecular-dynamics-based methods for building pseudo-atomic models in a semi-automated fashion. Among other features, our data allows discerning details such as helical grooves, single-strand versus double-strand crossovers, backbone phosphate positions, and single-strand breaks. Obtaining this higher level of detail is a step forward that now allows designers to inspect and refine their designs with base-pair level interventions.
History
DepositionOct 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Structure summary / Category: audit_author
Revision 1.2Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-11379
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AA: SCAFFOLD STRAND
AB: STAPLE STRAND
AC: STAPLE STRAND
AD: STAPLE STRAND
AE: STAPLE STRAND
AF: STAPLE STRAND
AG: STAPLE STRAND
AH: STAPLE STRAND
AI: STAPLE STRAND
AJ: STAPLE STRAND
AK: STAPLE STRAND
AL: STAPLE STRAND
AM: STAPLE STRAND
AN: STAPLE STRAND
AO: STAPLE STRAND
AP: STAPLE STRAND
AQ: STAPLE STRAND
AR: STAPLE STRAND
AS: STAPLE STRAND
AT: STAPLE STRAND
AU: STAPLE STRAND
AV: STAPLE STRAND
AW: STAPLE STRAND
AX: STAPLE STRAND
AY: STAPLE STRAND
AZ: STAPLE STRAND
Aa: STAPLE STRAND
Ab: STAPLE STRAND
Ac: STAPLE STRAND
Ad: STAPLE STRAND
Ae: STAPLE STRAND
Af: STAPLE STRAND
Ag: STAPLE STRAND
Ah: STAPLE STRAND
Ai: STAPLE STRAND
Aj: STAPLE STRAND
Ak: STAPLE STRAND
Al: STAPLE STRAND
Am: STAPLE STRAND
An: STAPLE STRAND
Ao: STAPLE STRAND
Ap: STAPLE STRAND
Aq: STAPLE STRAND
Ar: STAPLE STRAND
As: STAPLE STRAND
At: STAPLE STRAND
Au: STAPLE STRAND
Av: STAPLE STRAND
Aw: STAPLE STRAND
Ax: STAPLE STRAND
Ay: STAPLE STRAND
Az: STAPLE STRAND
A0: STAPLE STRAND
A1: STAPLE STRAND
A2: STAPLE STRAND
A3: STAPLE STRAND
A4: STAPLE STRAND
A5: STAPLE STRAND
A6: STAPLE STRAND
A7: STAPLE STRAND
A8: STAPLE STRAND
A9: STAPLE STRAND
BA: STAPLE STRAND
BB: STAPLE STRAND
BC: STAPLE STRAND
BD: STAPLE STRAND
BE: STAPLE STRAND
BF: STAPLE STRAND
BG: STAPLE STRAND
BH: STAPLE STRAND
BI: STAPLE STRAND
BJ: STAPLE STRAND
BK: STAPLE STRAND
BL: STAPLE STRAND
BM: STAPLE STRAND
BN: STAPLE STRAND
BO: STAPLE STRAND
BP: STAPLE STRAND
BQ: STAPLE STRAND
BR: STAPLE STRAND
BS: STAPLE STRAND
BT: STAPLE STRAND
BU: STAPLE STRAND
BV: STAPLE STRAND
BW: STAPLE STRAND
BX: STAPLE STRAND
BY: STAPLE STRAND
BZ: STAPLE STRAND
Ba: STAPLE STRAND
Bb: STAPLE STRAND
Bc: STAPLE STRAND
Bd: STAPLE STRAND
Be: STAPLE STRAND
Bf: STAPLE STRAND
Bg: STAPLE STRAND
Bh: STAPLE STRAND
Bi: STAPLE STRAND
Bj: STAPLE STRAND
Bk: STAPLE STRAND
Bl: STAPLE STRAND
Bm: STAPLE STRAND
Bn: STAPLE STRAND
Bo: STAPLE STRAND
Bp: STAPLE STRAND
Bq: STAPLE STRAND
Br: STAPLE STRAND
Bs: STAPLE STRAND
Bt: STAPLE STRAND
Bu: STAPLE STRAND
Bv: STAPLE STRAND
Bw: STAPLE STRAND
Bx: STAPLE STRAND
By: STAPLE STRAND
Bz: STAPLE STRAND
B0: STAPLE STRAND
B1: STAPLE STRAND
B2: STAPLE STRAND
B3: STAPLE STRAND
B4: STAPLE STRAND
B5: STAPLE STRAND
B6: STAPLE STRAND
B7: STAPLE STRAND
B8: STAPLE STRAND
B9: STAPLE STRAND
CA: STAPLE STRAND
CB: STAPLE STRAND
CC: STAPLE STRAND
CD: STAPLE STRAND
CE: STAPLE STRAND
CF: STAPLE STRAND
CG: STAPLE STRAND
CH: STAPLE STRAND
CI: STAPLE STRAND
CJ: STAPLE STRAND
CK: STAPLE STRAND
CL: STAPLE STRAND
CM: STAPLE STRAND
CN: STAPLE STRAND
CO: STAPLE STRAND
CP: STAPLE STRAND
CQ: STAPLE STRAND
CR: STAPLE STRAND
CS: STAPLE STRAND
CT: STAPLE STRAND
CU: STAPLE STRAND
CV: STAPLE STRAND
CW: STAPLE STRAND
CX: STAPLE STRAND
CY: STAPLE STRAND
CZ: STAPLE STRAND
Ca: STAPLE STRAND
Cb: STAPLE STRAND
Cc: STAPLE STRAND
Cd: STAPLE STRAND
Ce: STAPLE STRAND
Cf: STAPLE STRAND
Cg: STAPLE STRAND
Ch: STAPLE STRAND
Ci: STAPLE STRAND
Cj: STAPLE STRAND
Ck: STAPLE STRAND
Cl: STAPLE STRAND
Cm: STAPLE STRAND
Cn: STAPLE STRAND
Co: STAPLE STRAND
Cp: STAPLE STRAND
Cq: STAPLE STRAND
Cr: STAPLE STRAND
Cs: STAPLE STRAND
Ct: STAPLE STRAND
Cu: STAPLE STRAND
Cv: STAPLE STRAND
Cw: STAPLE STRAND
Cx: STAPLE STRAND
Cy: STAPLE STRAND
Cz: STAPLE STRAND
C0: STAPLE STRAND
C1: STAPLE STRAND
C2: STAPLE STRAND
C3: STAPLE STRAND
C4: STAPLE STRAND
C5: STAPLE STRAND
C6: STAPLE STRAND
C7: STAPLE STRAND
C8: STAPLE STRAND
C9: STAPLE STRAND
DA: STAPLE STRAND
DB: STAPLE STRAND
DC: STAPLE STRAND
DD: STAPLE STRAND
DE: STAPLE STRAND
DF: STAPLE STRAND
DG: STAPLE STRAND
DH: STAPLE STRAND
DI: STAPLE STRAND


Theoretical massNumber of molelcules
Total (without water)5,164,337195
Polymers5,164,337195
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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DNA chain , 195 types, 195 molecules AAABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAXAYAZAaAbAcAd...

#1: DNA chain SCAFFOLD STRAND


Mass: 2488158.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain STAPLE STRAND


Mass: 8808.652 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain STAPLE STRAND


Mass: 14824.511 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain STAPLE STRAND


Mass: 16459.602 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain STAPLE STRAND


Mass: 18387.736 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain STAPLE STRAND


Mass: 14799.497 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain STAPLE STRAND


Mass: 14907.575 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#8: DNA chain STAPLE STRAND


Mass: 18484.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#9: DNA chain STAPLE STRAND


Mass: 12850.281 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#10: DNA chain STAPLE STRAND


Mass: 18395.830 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#11: DNA chain STAPLE STRAND


Mass: 9903.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#12: DNA chain STAPLE STRAND


Mass: 12298.908 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#13: DNA chain STAPLE STRAND


Mass: 14862.611 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#14: DNA chain STAPLE STRAND


Mass: 9945.466 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#15: DNA chain STAPLE STRAND


Mass: 14727.526 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#16: DNA chain STAPLE STRAND


Mass: 12291.958 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#17: DNA chain STAPLE STRAND


Mass: 13796.887 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#18: DNA chain STAPLE STRAND


Mass: 14837.601 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#19: DNA chain STAPLE STRAND


Mass: 14858.591 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#20: DNA chain STAPLE STRAND


Mass: 13985.946 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#21: DNA chain STAPLE STRAND


Mass: 14728.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#22: DNA chain STAPLE STRAND


Mass: 12287.936 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#23: DNA chain STAPLE STRAND


Mass: 17485.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#24: DNA chain STAPLE STRAND


Mass: 18468.877 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#25: DNA chain STAPLE STRAND


Mass: 9921.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#26: DNA chain STAPLE STRAND


Mass: 14889.602 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#27: DNA chain STAPLE STRAND


Mass: 12395.994 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#28: DNA chain STAPLE STRAND


Mass: 14843.525 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#29: DNA chain STAPLE STRAND


Mass: 12232.918 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#30: DNA chain STAPLE STRAND


Mass: 16419.576 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#31: DNA chain STAPLE STRAND


Mass: 12483.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#32: DNA chain STAPLE STRAND


Mass: 10016.446 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#33: DNA chain STAPLE STRAND


Mass: 17723.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#34: DNA chain STAPLE STRAND


Mass: 18578.947 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#35: DNA chain STAPLE STRAND


Mass: 14774.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#36: DNA chain STAPLE STRAND


Mass: 14622.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#37: DNA chain STAPLE STRAND


Mass: 9818.355 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#38: DNA chain STAPLE STRAND


Mass: 14783.552 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#39: DNA chain STAPLE STRAND


Mass: 17757.363 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#40: DNA chain STAPLE STRAND


Mass: 18560.922 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#41: DNA chain STAPLE STRAND


Mass: 17599.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#42: DNA chain STAPLE STRAND


Mass: 18403.748 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#43: DNA chain STAPLE STRAND


Mass: 14841.497 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#44: DNA chain STAPLE STRAND


Mass: 11333.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#45: DNA chain STAPLE STRAND


Mass: 12320.955 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#46: DNA chain STAPLE STRAND


Mass: 13531.766 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#47: DNA chain STAPLE STRAND


Mass: 12306.970 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#48: DNA chain STAPLE STRAND


Mass: 12267.878 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#49: DNA chain STAPLE STRAND


Mass: 17157.000 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#50: DNA chain STAPLE STRAND


Mass: 12291.922 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#51: DNA chain STAPLE STRAND


Mass: 14883.603 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#52: DNA chain STAPLE STRAND


Mass: 13597.739 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#53: DNA chain STAPLE STRAND


Mass: 9688.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#54: DNA chain STAPLE STRAND


Mass: 14921.598 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#55: DNA chain STAPLE STRAND


Mass: 14589.307 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#56: DNA chain STAPLE STRAND


Mass: 17324.115 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#57: DNA chain STAPLE STRAND


Mass: 14017.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#58: DNA chain STAPLE STRAND


Mass: 14906.589 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#59: DNA chain STAPLE STRAND


Mass: 9872.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#60: DNA chain STAPLE STRAND


Mass: 9693.274 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#61: DNA chain STAPLE STRAND


Mass: 9900.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#62: DNA chain STAPLE STRAND


Mass: 14861.556 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#63: DNA chain STAPLE STRAND


Mass: 13815.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#64: DNA chain STAPLE STRAND


Mass: 9910.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#65: DNA chain STAPLE STRAND


Mass: 13744.815 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#66: DNA chain STAPLE STRAND


Mass: 17467.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#67: DNA chain STAPLE STRAND


Mass: 17439.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#68: DNA chain STAPLE STRAND


Mass: 13755.805 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#69: DNA chain STAPLE STRAND


Mass: 12169.859 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#70: DNA chain STAPLE STRAND


Mass: 17471.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#71: DNA chain STAPLE STRAND


Mass: 17443.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#72: DNA chain STAPLE STRAND


Mass: 13846.912 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#73: DNA chain STAPLE STRAND


Mass: 9872.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#74: DNA chain STAPLE STRAND


Mass: 17227.045 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#75: DNA chain STAPLE STRAND


Mass: 9779.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#76: DNA chain STAPLE STRAND


Mass: 12486.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#77: DNA chain STAPLE STRAND


Mass: 14683.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#78: DNA chain STAPLE STRAND


Mass: 17736.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#79: DNA chain STAPLE STRAND


Mass: 17333.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#80: DNA chain STAPLE STRAND


Mass: 14959.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#81: DNA chain STAPLE STRAND


Mass: 14707.472 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#82: DNA chain STAPLE STRAND


Mass: 14680.412 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#83: DNA chain STAPLE STRAND


Mass: 14786.463 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#84: DNA chain STAPLE STRAND


Mass: 17887.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#85: DNA chain STAPLE STRAND


Mass: 18343.705 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#86: DNA chain STAPLE STRAND


Mass: 9892.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#87: DNA chain STAPLE STRAND


Mass: 12506.982 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#88: DNA chain STAPLE STRAND


Mass: 12323.903 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#89: DNA chain STAPLE STRAND


Mass: 15035.726 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#90: DNA chain STAPLE STRAND


Mass: 14649.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#91: DNA chain STAPLE STRAND


Mass: 9892.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#92: DNA chain STAPLE STRAND


Mass: 14892.669 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#93: DNA chain STAPLE STRAND


Mass: 14710.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#94: DNA chain STAPLE STRAND


Mass: 14834.563 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#95: DNA chain STAPLE STRAND


Mass: 12254.860 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#96: DNA chain STAPLE STRAND


Mass: 17400.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#97: DNA chain STAPLE STRAND


Mass: 12162.836 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#98: DNA chain STAPLE STRAND


Mass: 9826.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#99: DNA chain STAPLE STRAND


Mass: 9928.426 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#100: DNA chain STAPLE STRAND


Mass: 14698.389 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#101: DNA chain STAPLE STRAND


Mass: 17309.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#102: DNA chain STAPLE STRAND


Mass: 14647.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#103: DNA chain STAPLE STRAND


Mass: 14933.627 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#104: DNA chain STAPLE STRAND


Mass: 12375.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#105: DNA chain STAPLE STRAND


Mass: 14883.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#106: DNA chain STAPLE STRAND


Mass: 14929.569 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#107: DNA chain STAPLE STRAND


Mass: 9820.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#108: DNA chain STAPLE STRAND


Mass: 12386.965 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#109: DNA chain STAPLE STRAND


Mass: 12322.969 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#110: DNA chain STAPLE STRAND


Mass: 12241.880 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#111: DNA chain STAPLE STRAND


Mass: 18364.814 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#112: DNA chain STAPLE STRAND


Mass: 13852.896 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#113: DNA chain STAPLE STRAND


Mass: 12367.987 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#114: DNA chain STAPLE STRAND


Mass: 9853.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#115: DNA chain STAPLE STRAND


Mass: 18291.758 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#116: DNA chain STAPLE STRAND


Mass: 18340.742 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#117: DNA chain STAPLE STRAND


Mass: 12371.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#118: DNA chain STAPLE STRAND


Mass: 9973.443 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#119: DNA chain STAPLE STRAND


Mass: 9971.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#120: DNA chain STAPLE STRAND


Mass: 18436.879 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#121: DNA chain STAPLE STRAND


Mass: 16236.444 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#122: DNA chain STAPLE STRAND


Mass: 14772.547 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#123: DNA chain STAPLE STRAND


Mass: 9892.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#124: DNA chain STAPLE STRAND


Mass: 14699.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#125: DNA chain STAPLE STRAND


Mass: 14737.423 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#126: DNA chain STAPLE STRAND


Mass: 18434.902 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#127: DNA chain STAPLE STRAND


Mass: 11372.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#128: DNA chain STAPLE STRAND


Mass: 17526.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#129: DNA chain STAPLE STRAND


Mass: 10029.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#130: DNA chain STAPLE STRAND


Mass: 12362.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#131: DNA chain STAPLE STRAND


Mass: 9904.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#132: DNA chain STAPLE STRAND


Mass: 16356.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#133: DNA chain STAPLE STRAND


Mass: 9748.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#134: DNA chain STAPLE STRAND


Mass: 17498.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#135: DNA chain STAPLE STRAND


Mass: 9792.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#136: DNA chain STAPLE STRAND


Mass: 12316.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#137: DNA chain STAPLE STRAND


Mass: 9971.467 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#138: DNA chain STAPLE STRAND


Mass: 17342.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#139: DNA chain STAPLE STRAND


Mass: 14732.522 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#140: DNA chain STAPLE STRAND


Mass: 14941.565 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#141: DNA chain STAPLE STRAND


Mass: 17539.277 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#142: DNA chain STAPLE STRAND


Mass: 18478.895 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#143: DNA chain STAPLE STRAND


Mass: 14625.395 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#144: DNA chain STAPLE STRAND


Mass: 17414.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#145: DNA chain STAPLE STRAND


Mass: 11414.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#146: DNA chain STAPLE STRAND


Mass: 9873.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#147: DNA chain STAPLE STRAND


Mass: 9816.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#148: DNA chain STAPLE STRAND


Mass: 17512.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#149: DNA chain STAPLE STRAND


Mass: 18297.809 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#150: DNA chain STAPLE STRAND


Mass: 14787.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#151: DNA chain STAPLE STRAND


Mass: 14785.633 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#152: DNA chain STAPLE STRAND


Mass: 12346.993 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#153: DNA chain STAPLE STRAND


Mass: 9864.378 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#154: DNA chain STAPLE STRAND


Mass: 12471.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#155: DNA chain STAPLE STRAND


Mass: 12470.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#156: DNA chain STAPLE STRAND


Mass: 9901.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#157: DNA chain STAPLE STRAND


Mass: 12295.979 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#158: DNA chain STAPLE STRAND


Mass: 12301.976 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#159: DNA chain STAPLE STRAND


Mass: 14640.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#160: DNA chain STAPLE STRAND


Mass: 12304.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#161: DNA chain STAPLE STRAND


Mass: 14849.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#162: DNA chain STAPLE STRAND


Mass: 12346.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#163: DNA chain STAPLE STRAND


Mass: 14772.509 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#164: DNA chain STAPLE STRAND


Mass: 12334.962 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#165: DNA chain STAPLE STRAND


Mass: 12218.896 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#166: DNA chain STAPLE STRAND


Mass: 11333.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#167: DNA chain STAPLE STRAND


Mass: 11352.339 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#168: DNA chain STAPLE STRAND


Mass: 12512.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#169: DNA chain STAPLE STRAND


Mass: 12362.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#170: DNA chain STAPLE STRAND


Mass: 13864.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#171: DNA chain STAPLE STRAND


Mass: 11394.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#172: DNA chain STAPLE STRAND


Mass: 12228.859 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#173: DNA chain STAPLE STRAND


Mass: 12411.979 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#174: DNA chain STAPLE STRAND


Mass: 9813.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#175: DNA chain STAPLE STRAND


Mass: 9814.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#176: DNA chain STAPLE STRAND


Mass: 10026.449 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#177: DNA chain STAPLE STRAND


Mass: 17346.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#178: DNA chain STAPLE STRAND


Mass: 17601.295 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#179: DNA chain STAPLE STRAND


Mass: 9888.403 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#180: DNA chain STAPLE STRAND


Mass: 14740.493 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#181: DNA chain STAPLE STRAND


Mass: 14718.515 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#182: DNA chain STAPLE STRAND


Mass: 14723.472 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#183: DNA chain STAPLE STRAND


Mass: 14986.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#184: DNA chain STAPLE STRAND


Mass: 12132.813 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#185: DNA chain STAPLE STRAND


Mass: 14898.612 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#186: DNA chain STAPLE STRAND


Mass: 17483.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#187: DNA chain STAPLE STRAND


Mass: 13826.891 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#188: DNA chain STAPLE STRAND


Mass: 9738.308 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#189: DNA chain STAPLE STRAND


Mass: 12471.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#190: DNA chain STAPLE STRAND


Mass: 13740.794 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#191: DNA chain STAPLE STRAND


Mass: 14790.536 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#192: DNA chain STAPLE STRAND


Mass: 12306.915 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#193: DNA chain STAPLE STRAND


Mass: 14904.559 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#194: DNA chain STAPLE STRAND


Mass: 9829.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#195: DNA chain STAPLE STRAND


Mass: 9839.363 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: TwistTower_native-twist / Type: COMPLEX
Details: multilayer DNA origami object consisting of 4 domains with cross sections of 2x2, 4x4, 6x6, and 8x8 helices arranged on a square lattice. Designed with native crossover spacing corresponding to 10.66bp/turn.
Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: synthetic construct (others)
Source (recombinant)Organism: synthetic construct (others)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: monodisperse, 5 datasets: 1.5uM, 1.0uM, 2.3uM, 2.0uM, 1.75uM
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-2/1
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 47000 X / Nominal defocus max: 3692 nm / Calibrated defocus min: 260.5 nm / Cs: 0.01 mm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 55 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 21279 / Details: magnified pixel size 1.39 A
EM imaging opticsSpherical aberration corrector: CEOS Cs corrector
Image scansWidth: 4096 / Height: 4096

-
Processing

EM software
IDNameVersionCategory
1CTFFIND4.1particle selection
13RELION23D reconstruction
14RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 7.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 509812
Details: Resolution of individual domains (Multibody Refinement): 2x2: 7.8 A, 4x4: 6.5 A, 6x6: 6.8 A, 8x8: 7.1 A -> composite map: 7.0 A (weighted average)
Symmetry type: POINT

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