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- PDB-7ary: Twist-Tower_twist-corrected-variant -

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Basic information

Entry
Database: PDB / ID: 7ary
TitleTwist-Tower_twist-corrected-variant
Components
  • (STAPLE STRAND) x 191
  • 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: 8.5 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-11378
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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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


Theoretical massNumber of molelcules
Total (without water)5,003,104192
Polymers5,003,104192
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 , 192 types, 192 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: 14609.433 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain STAPLE STRAND


Mass: 16407.578 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain STAPLE STRAND


Mass: 14880.586 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain STAPLE STRAND


Mass: 14655.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain STAPLE STRAND


Mass: 17015.973 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain STAPLE STRAND


Mass: 14668.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#8: DNA chain STAPLE STRAND


Mass: 9573.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#9: DNA chain STAPLE STRAND


Mass: 8606.558 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#10: DNA chain STAPLE STRAND


Mass: 14727.474 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#11: DNA chain STAPLE STRAND


Mass: 9898.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#12: DNA chain STAPLE STRAND


Mass: 16055.303 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#13: DNA chain STAPLE STRAND


Mass: 11573.482 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#14: DNA chain STAPLE STRAND


Mass: 14244.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#15: DNA chain STAPLE STRAND


Mass: 14228.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#16: DNA chain STAPLE STRAND


Mass: 14805.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#17: DNA chain STAPLE STRAND


Mass: 14677.466 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#18: DNA chain STAPLE STRAND


Mass: 14196.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#19: DNA chain STAPLE STRAND


Mass: 15248.881 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#20: DNA chain STAPLE STRAND


Mass: 14434.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#21: DNA chain STAPLE STRAND


Mass: 12372.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#22: DNA chain STAPLE STRAND


Mass: 13858.907 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#23: DNA chain STAPLE STRAND


Mass: 14787.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#24: DNA chain STAPLE STRAND


Mass: 11468.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#25: DNA chain STAPLE STRAND


Mass: 14538.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#26: DNA chain STAPLE STRAND


Mass: 12250.893 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#27: DNA chain STAPLE STRAND


Mass: 16349.533 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#28: DNA chain STAPLE STRAND


Mass: 12021.756 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#29: DNA chain STAPLE STRAND


Mass: 9423.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#30: DNA chain STAPLE STRAND


Mass: 13921.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#31: DNA chain STAPLE STRAND


Mass: 15948.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#32: DNA chain STAPLE STRAND


Mass: 14109.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#33: DNA chain STAPLE STRAND


Mass: 9283.984 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#34: DNA chain STAPLE STRAND


Mass: 12051.760 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#35: DNA chain STAPLE STRAND


Mass: 14812.496 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#36: DNA chain STAPLE STRAND


Mass: 12324.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#37: DNA chain STAPLE STRAND


Mass: 11671.542 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#38: DNA chain STAPLE STRAND


Mass: 17119.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#39: DNA chain STAPLE STRAND


Mass: 11654.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#40: DNA chain STAPLE STRAND


Mass: 13751.838 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#41: DNA chain STAPLE STRAND


Mass: 14176.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#42: DNA chain STAPLE STRAND


Mass: 14698.459 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#43: DNA chain STAPLE STRAND


Mass: 9945.467 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#44: DNA chain STAPLE STRAND


Mass: 14875.593 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#45: DNA chain STAPLE STRAND


Mass: 14878.647 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#46: DNA chain STAPLE STRAND


Mass: 16631.732 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#47: DNA chain STAPLE STRAND


Mass: 14074.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#48: DNA chain STAPLE STRAND


Mass: 14815.602 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#49: DNA chain STAPLE STRAND


Mass: 14577.346 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#50: DNA chain STAPLE STRAND


Mass: 13792.952 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#51: DNA chain STAPLE STRAND


Mass: 9660.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#52: DNA chain STAPLE STRAND


Mass: 9224.981 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#53: DNA chain STAPLE STRAND


Mass: 9749.297 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#54: DNA chain STAPLE STRAND


Mass: 14808.564 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#55: DNA chain STAPLE STRAND


Mass: 14151.192 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#56: DNA chain STAPLE STRAND


Mass: 9255.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#57: DNA chain STAPLE STRAND


Mass: 13771.909 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#58: DNA chain STAPLE STRAND


Mass: 13895.016 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#59: DNA chain STAPLE STRAND


Mass: 14930.666 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#60: DNA chain STAPLE STRAND


Mass: 14728.533 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#61: DNA chain STAPLE STRAND


Mass: 18242.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#62: DNA chain STAPLE STRAND


Mass: 11705.567 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#63: DNA chain STAPLE STRAND


Mass: 14746.543 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#64: DNA chain STAPLE STRAND


Mass: 9572.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#65: DNA chain STAPLE STRAND


Mass: 18436.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#66: DNA chain STAPLE STRAND


Mass: 16358.598 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#67: DNA chain STAPLE STRAND


Mass: 9761.347 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#68: DNA chain STAPLE STRAND


Mass: 11705.622 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#69: DNA chain STAPLE STRAND


Mass: 14472.284 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#70: DNA chain STAPLE STRAND


Mass: 17520.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#71: DNA chain STAPLE STRAND


Mass: 13815.885 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#72: DNA chain STAPLE STRAND


Mass: 13942.995 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#73: DNA chain STAPLE STRAND


Mass: 14782.513 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#74: DNA chain STAPLE STRAND


Mass: 13834.917 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#75: DNA chain STAPLE STRAND


Mass: 14886.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#76: DNA chain STAPLE STRAND


Mass: 9295.027 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#77: DNA chain STAPLE STRAND


Mass: 13780.873 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#78: DNA chain STAPLE STRAND


Mass: 13839.963 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#79: DNA chain STAPLE STRAND


Mass: 13967.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#80: DNA chain STAPLE STRAND


Mass: 11620.474 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#81: DNA chain STAPLE STRAND


Mass: 14658.484 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#82: DNA chain STAPLE STRAND


Mass: 16090.355 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#83: DNA chain STAPLE STRAND


Mass: 11840.599 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#84: DNA chain STAPLE STRAND


Mass: 9758.274 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#85: DNA chain STAPLE STRAND


Mass: 9412.066 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#86: DNA chain STAPLE STRAND


Mass: 13757.887 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#87: DNA chain STAPLE STRAND


Mass: 16033.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#88: DNA chain STAPLE STRAND


Mass: 14385.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#89: DNA chain STAPLE STRAND


Mass: 14306.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#90: DNA chain STAPLE STRAND


Mass: 11873.691 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#91: DNA chain STAPLE STRAND


Mass: 13904.963 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#92: DNA chain STAPLE STRAND


Mass: 14808.616 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#93: DNA chain STAPLE STRAND


Mass: 13683.822 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#94: DNA chain STAPLE STRAND


Mass: 11690.573 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#95: DNA chain STAPLE STRAND


Mass: 11783.588 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#96: DNA chain STAPLE STRAND


Mass: 12245.937 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#97: DNA chain STAPLE STRAND


Mass: 14997.659 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#98: DNA chain STAPLE STRAND


Mass: 14888.665 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#99: DNA chain STAPLE STRAND


Mass: 9313.056 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#100: DNA chain STAPLE STRAND


Mass: 12452.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#101: DNA chain STAPLE STRAND


Mass: 11633.549 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#102: DNA chain STAPLE STRAND


Mass: 13229.567 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#103: DNA chain STAPLE STRAND


Mass: 13794.911 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#104: DNA chain STAPLE STRAND


Mass: 14634.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#105: DNA chain STAPLE STRAND


Mass: 14847.511 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#106: DNA chain STAPLE STRAND


Mass: 11722.570 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#107: DNA chain STAPLE STRAND


Mass: 9192.947 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#108: DNA chain STAPLE STRAND


Mass: 13860.934 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#109: DNA chain STAPLE STRAND


Mass: 15141.757 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#110: DNA chain STAPLE STRAND


Mass: 12269.910 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#111: DNA chain STAPLE STRAND


Mass: 11322.386 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#112: DNA chain STAPLE STRAND


Mass: 15989.297 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#113: DNA chain STAPLE STRAND


Mass: 9385.077 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#114: DNA chain STAPLE STRAND


Mass: 12339.021 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#115: DNA chain STAPLE STRAND


Mass: 9229.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#116: DNA chain STAPLE STRAND


Mass: 16067.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#117: DNA chain STAPLE STRAND


Mass: 9239.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#118: DNA chain STAPLE STRAND


Mass: 17218.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#119: DNA chain STAPLE STRAND


Mass: 14861.552 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#120: DNA chain STAPLE STRAND


Mass: 9529.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#121: DNA chain STAPLE STRAND


Mass: 13986.988 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#122: DNA chain STAPLE STRAND


Mass: 11455.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#123: DNA chain STAPLE STRAND


Mass: 16086.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#124: DNA chain STAPLE STRAND


Mass: 11602.448 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#125: DNA chain STAPLE STRAND


Mass: 9716.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#126: DNA chain STAPLE STRAND


Mass: 9881.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#127: DNA chain STAPLE STRAND


Mass: 9378.039 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#128: DNA chain STAPLE STRAND


Mass: 18116.582 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#129: DNA chain STAPLE STRAND


Mass: 15993.338 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#130: DNA chain STAPLE STRAND


Mass: 12278.925 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#131: DNA chain STAPLE STRAND


Mass: 9452.037 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#132: DNA chain STAPLE STRAND


Mass: 16531.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#133: DNA chain STAPLE STRAND


Mass: 9247.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#134: DNA chain STAPLE STRAND


Mass: 14952.589 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#135: DNA chain STAPLE STRAND


Mass: 17204.953 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#136: DNA chain STAPLE STRAND


Mass: 9633.194 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#137: DNA chain STAPLE STRAND


Mass: 9828.359 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#138: DNA chain STAPLE STRAND


Mass: 12427.041 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#139: DNA chain STAPLE STRAND


Mass: 9158.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#140: DNA chain STAPLE STRAND


Mass: 16683.641 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#141: DNA chain STAPLE STRAND


Mass: 14714.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#142: DNA chain STAPLE STRAND


Mass: 13906.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#143: DNA chain STAPLE STRAND


Mass: 14811.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#144: DNA chain STAPLE STRAND


Mass: 11594.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#145: DNA chain STAPLE STRAND


Mass: 9306.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#146: DNA chain STAPLE STRAND


Mass: 9821.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#147: DNA chain STAPLE STRAND


Mass: 14599.378 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#148: DNA chain STAPLE STRAND


Mass: 14710.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#149: DNA chain STAPLE STRAND


Mass: 14959.576 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#150: DNA chain STAPLE STRAND


Mass: 14294.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#151: DNA chain STAPLE STRAND


Mass: 12003.765 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#152: DNA chain STAPLE STRAND


Mass: 14019.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#153: DNA chain STAPLE STRAND


Mass: 9286.947 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#154: DNA chain STAPLE STRAND


Mass: 11731.515 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#155: DNA chain STAPLE STRAND


Mass: 9111.841 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#156: DNA chain STAPLE STRAND


Mass: 12107.837 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#157: DNA chain STAPLE STRAND


Mass: 11735.539 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#158: DNA chain STAPLE STRAND


Mass: 13966.968 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#159: DNA chain STAPLE STRAND


Mass: 14768.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#160: DNA chain STAPLE STRAND


Mass: 16680.660 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#161: DNA chain STAPLE STRAND


Mass: 14257.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#162: DNA chain STAPLE STRAND


Mass: 13781.806 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#163: DNA chain STAPLE STRAND


Mass: 11569.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#164: DNA chain STAPLE STRAND


Mass: 13785.916 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#165: DNA chain STAPLE STRAND


Mass: 11351.313 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#166: DNA chain STAPLE STRAND


Mass: 11350.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#167: DNA chain STAPLE STRAND


Mass: 11035.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#168: DNA chain STAPLE STRAND


Mass: 11726.522 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#169: DNA chain STAPLE STRAND


Mass: 12119.727 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#170: DNA chain STAPLE STRAND


Mass: 11739.598 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#171: DNA chain STAPLE STRAND


Mass: 11103.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#172: DNA chain STAPLE STRAND


Mass: 11305.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#173: DNA chain STAPLE STRAND


Mass: 9468.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#174: DNA chain STAPLE STRAND


Mass: 11432.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#175: DNA chain STAPLE STRAND


Mass: 13830.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#176: DNA chain STAPLE STRAND


Mass: 16013.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#177: DNA chain STAPLE STRAND


Mass: 18364.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#178: DNA chain STAPLE STRAND


Mass: 14518.342 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#179: DNA chain STAPLE STRAND


Mass: 9928.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#180: DNA chain STAPLE STRAND


Mass: 11407.321 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#181: DNA chain STAPLE STRAND


Mass: 17501.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#182: DNA chain STAPLE STRAND


Mass: 13676.851 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#183: DNA chain STAPLE STRAND


Mass: 14441.312 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#184: DNA chain STAPLE STRAND


Mass: 14404.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#185: DNA chain STAPLE STRAND


Mass: 11631.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#186: DNA chain STAPLE STRAND


Mass: 11510.458 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#187: DNA chain STAPLE STRAND


Mass: 18455.898 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#188: DNA chain STAPLE STRAND


Mass: 13218.454 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#189: DNA chain STAPLE STRAND


Mass: 14291.271 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#190: DNA chain STAPLE STRAND


Mass: 11680.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#191: DNA chain STAPLE STRAND


Mass: 14155.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#192: DNA chain STAPLE STRAND


Mass: 9594.211 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_twist-corrected-vaiant DNA nanostructure / Type: COMPLEX
Details: multilayer DNA origami nanoobject consisting of 4 domains with crosssections of 2x2, 4x4, 6x6, and 8x8 helices arranged on a square lattice. Twist corrected variant using 1 "skip" per 32bp ...Details: multilayer DNA origami nanoobject consisting of 4 domains with crosssections of 2x2, 4x4, 6x6, and 8x8 helices arranged on a square lattice. Twist corrected variant using 1 "skip" per 32bp segment corresponding to a periodicity of 10.33bp/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, 900nM
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Details: CEOS Cs corrector
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 47000 X / Calibrated defocus min: 328.5 nm / Calibrated defocus max: 2444.2 nm / Cs: 0.01 mm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 51 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 5911 / Details: magnified pixel size 1.39 A
Image scansWidth: 4096 / Height: 4096

-
Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4.1CTF correction
11RELION2final Euler assignment
12RELION3final Euler assignment
14RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 8.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 94834
Details: Resolution of domains (Multibody Refinement): 2x2: 10.0A, 4x4: 7.7A, 6x6: 8.1A, 8x8: 8.0A -> composite map: 8.1 A (weighted average)
Symmetry type: POINT

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