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- EMDB-2210: The cryo-EM structure of a 3D DNA-origami object -

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Basic information

Entry
Database: EMDB / ID: EMD-2210
TitleThe cryo-EM structure of a 3D DNA-origami object
Map dataA 3D-origami object
Sample
  • Sample: A pointer-shaped 3D DNA-origami object, for convenience termed "pointer"
  • DNA: M13 phage genome
  • DNA: synthetic DNA segments
KeywordsDNA-templated design / Synthetic biology / 3D DNA origami
Biological speciesEnterobacteria phage M13 (virus) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.5 Å
AuthorsBai XC / Martin TG / Scheres SHW / Dietz H
CitationJournal: Proc Natl Acad Sci U S A / Year: 2012
Title: Cryo-EM structure of a 3D DNA-origami object.
Authors: Xiao-Chen Bai / Thomas G Martin / Sjors H W Scheres / Hendrik Dietz /
Abstract: A key goal for nanotechnology is to design synthetic objects that may ultimately achieve functionalities known today only from natural macromolecular complexes. Molecular self-assembly with DNA has ...A key goal for nanotechnology is to design synthetic objects that may ultimately achieve functionalities known today only from natural macromolecular complexes. Molecular self-assembly with DNA has shown potential for creating user-defined 3D scaffolds, but the level of attainable positional accuracy has been unclear. Here we report the cryo-EM structure and a full pseudoatomic model of a discrete DNA object that is almost twice the size of a prokaryotic ribosome. The structure provides a variety of stable, previously undescribed DNA topologies for future use in nanotechnology and experimental evidence that discrete 3D DNA scaffolds allow the positioning of user-defined structural motifs with an accuracy that is similar to that observed in natural macromolecules. Thereby, our results indicate an attractive route to fabricate nanoscale devices that achieve complex functionalities by DNA-templated design steered by structural feedback.
History
DepositionOct 8, 2012-
Header (metadata) releaseOct 24, 2012-
Map releaseNov 28, 2012-
UpdateDec 12, 2012-
Current statusDec 12, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-4v5x
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2210.png

Downloads & links

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Map

FileDownload / File: emd_2210.map.gz / Format: CCP4 / Size: 19 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA 3D-origami object
Voxel sizeX=Y=Z: 3.55 Å
Density
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.31412318 - 0.50923872
Average (Standard dev.)0.00337955 (±0.03246282)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions172172172
Spacing172172172
CellA=B=C: 610.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.553.553.55
M x/y/z172172172
origin x/y/z0.0000.0000.000
length x/y/z610.600610.600610.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS172172172
D min/max/mean-0.3140.5090.003

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Supplemental data

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Sample components

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Entire : A pointer-shaped 3D DNA-origami object, for convenience termed "p...

EntireName: A pointer-shaped 3D DNA-origami object, for convenience termed "pointer"
Components
  • Sample: A pointer-shaped 3D DNA-origami object, for convenience termed "pointer"
  • DNA: M13 phage genome
  • DNA: synthetic DNA segments

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Supramolecule #1000: A pointer-shaped 3D DNA-origami object, for convenience termed "p...

SupramoleculeName: A pointer-shaped 3D DNA-origami object, for convenience termed "pointer"
type: sample / ID: 1000
Details: A highly pure and monodisperse sample was obtained in a one-pot overnight reaction, followed by molecular weight cut-off filtration (with 100kDa filters)
Oligomeric state: monomer / Number unique components: 164
Molecular weightExperimental: 4.8 MDa / Theoretical: 4.8 MDa / Method: Calculation

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Macromolecule #1: M13 phage genome

MacromoleculeName: M13 phage genome / type: dna / ID: 1 / Name.synonym: Scaffold strand / Details: isolated M13 phage genome / Classification: DNA / Structure: SINGLE STRANDED / Synthetic?: No
Source (natural)Organism: Enterobacteria phage M13 (virus) / synonym: M13 phage
Molecular weightExperimental: 2.4 MDa / Theoretical: 2.4 MDa
SequenceString: TGATAGACGG TTTTTCGCCC TTTGACGTTG GAGTCCACGT TCTTTAATAG TGGACTCTTG TTCCAAACTG GAACAACACT CAACCCTATC TCGGGCTATT CTTTTGATTT ATAAGGGATT TTGCCGATTT CGGAACCACC ATCAAACAGG ATTTTCGCCT GCTGGGGCAA ...String:
TGATAGACGG TTTTTCGCCC TTTGACGTTG GAGTCCACGT TCTTTAATAG TGGACTCTTG TTCCAAACTG GAACAACACT CAACCCTATC TCGGGCTATT CTTTTGATTT ATAAGGGATT TTGCCGATTT CGGAACCACC ATCAAACAGG ATTTTCGCCT GCTGGGGCAA ACCAGCGTGG ACCGCTTGCT GCAACTCTCT CAGGGCCAGG CGGTGAAGGG CAATCAGCTG TTGCCCGTCT CACTGGTGAA AAGAAAAACC ACCCTGGCGC CCAATACGCA AACCGCCTCT CCCCGCGCGT TGGCCGATTC ATTAATGCAG CTGGCACGAC AGGTTTCCCG ACTGGAAAGC GGGCAGTGAG CGCAACGCAA TTAATGTGAG TTAGCTCACT CATTAGGCAC CCCAGGCTTT ACACTTTATG CTTCCGGCTC GTATGTTGTG TGGAATTGTG AGCGGATAAC AATTTCACAC AGGAAACAGC TATGACCATG ATTACGAATT CGAGCTCGGT ACCCGGGGAT CCTCTAGAGT CGACCTGCAG GCATGCAAGC TTGGCACTGG CCGTCGTTTT ACAACGTCGT GACTGGGAAA ACCCTGGCGT TACCCAACTT AATCGCCTTG CAGCACATCC CCCTTTCGCC AGCTGGCGTA ATAGCGAAGA GGCCCGCACC GATCGCCCTT CCCAACAGTT GCGCAGCCTG AATGGCGAAT GGCGCTTTGC CTGGTTTCCG GCACCAGAAG CGGTGCCGGA AAGCTGGCTG GAGTGCGATC TTCCTGAGGC CGATACTGTC GTCGTCCCCT CAAACTGGCA GATGCACGGT TACGATGCGC CCATCTACAC CAACGTGACC TATCCCATTA CGGTCAATCC GCCGTTTGTT CCCACGGAGA ATCCGACGGG TTGTTACTCG CTCACATTTA ATGTTGATGA AAGCTGGCTA CAGGAAGGCC AGACGCGAAT TATTTTTGAT GGCGTTCCTA TTGGTTAAAA AATGAGCTGA TTTAACAAAA ATTTAATGCG AATTTTAACA AAATATTAAC GTTTACAATT TAAATATTTG CTTATACAAT CTTCCTGTTT TTGGGGCTTT TCTGATTATC AACCGGGGTA CATATGATTG ACATGCTAGT TTTACGATTA CCGTTCATCG ATTCTCTTGT TTGCTCCAGA CTCTCAGGCA ATGACCTGAT AGCCTTTGTA GATCTCTCAA AAATAGCTAC CCTCTCCGGC ATTAATTTAT CAGCTAGAAC GGTTGAATAT CATATTGATG GTGATTTGAC TGTCTCCGGC CTTTCTCACC CTTTTGAATC TTTACCTACA CATTACTCAG GCATTGCATT TAAAATATAT GAGGGTTCTA AAAATTTTTA TCCTTGCGTT GAAATAAAGG CTTCTCCCGC AAAAGTATTA CAGGGTCATA ATGTTTTTGG TACAACCGAT TTAGCTTTAT GCTCTGAGGC TTTATTGCTT AATTTTGCTA ATTCTTTGCC TTGCCTGTAT GATTTATTGG ATGTTAATGC TACTACTATT AGTAGAATTG ATGCCACCTT TTCAGCTCGC GCCCCAAATG AAAATATAGC TAAACAGGTT ATTGACCATT TGCGAAATGT ATCTAATGGT CAAACTAAAT CTACTCGTTC GCAGAATTGG GAATCAACTG TTATATGGAA TGAAACTTCC AGACACCGTA CTTTAGTTGC ATATTTAAAA CATGTTGAGC TACAGCATTA TATTCAGCAA TTAAGCTCTA AGCCATCCGC AAAAATGACC TCTTATCAAA AGGAGCAATT AAAGGTACTC TCTAATCCTG ACCTGTTGGA GTTTGCTTCC GGTCTGGTTC GCTTTGAAGC TCGAATTAAA ACGCGATATT TGAAGTCTTT CGGGCTTCCT CTTAATCTTT TTGATGCAAT CCGCTTTGCT TCTGACTATA ATAGTCAGGG TAAAGACCTG ATTTTTGATT TATGGTCATT CTCGTTTTCT GAACTGTTTA AAGCATTTGA GGGGGATTCA ATGAATATTT ATGACGATTC CGCAGTATTG GACGCTATCC AGTCTAAACA TTTTACTATT ACCCCCTCTG GCAAAACTTC TTTTGCAAAA GCCTCTCGCT ATTTTGGTTT TTATCGTCGT CTGGTAAACG AGGGTTATGA TAGTGTTGCT CTTACTATGC CTCGTAATTC CTTTTGGCGT TATGTATCTG CATTAGTTGA ATGTGGTATT CCTAAATCTC AACTGATGAA TCTTTCTACC TGTAATAATG TTGTTCCGTT AGTTCGTTTT ATTAACGTAG ATTTTTCTTC CCAACGTCCT GACTGGTATA ATGAGCCAGT TCTTAAAATC GCATAAGGTA ATTCACAATG ATTAAAGTTG AAATTAAACC ATCTCAAGCC CAATTTACTA CTCGTTCTGG TGTTTCTCGT CAGGGCAAGC CTTATTCACT GAATGAGCAG CTTTGTTACG TTGATTTGGG TAATGAATAT CCGGTTCTTG TCAAGATTAC TCTTGATGAA GGTCAGCCAG CCTATGCGCC TGGTCTGTAC ACCGTTCATC TGTCCTCTTT CAAAGTTGGT CAGTTCGGTT CCCTTATGAT TGACCGTCTG CGCCTCGTTC CGGCTAAGTA ACATGGAGCA GGTCGCGGAT TTCGACACAA TTTATCAGGC GATGATACAA ATCTCCGTTG TACTTTGTTT CGCGCTTGGT ATAATCGCTG GGGGTCAAAG ATGAGTGTTT TAGTGTATTC TTTTGCCTCT TTCGTTTTAG GTTGGTGCCT TCGTAGTGGC ATTACGTATT TTACCCGTTT AATGGAAACT TCCTCATGAA AAAGTCTTTA GTCCTCAAAG CCTCTGTAGC CGTTGCTACC CTCGTTCCGA TGCTGTCTTT CGCTGCTGAG GGTGACGATC CCGCAAAAGC GGCCTTTAAC TCCCTGCAAG CCTCAGCGAC CGAATATATC GGTTATGCGT GGGCGATGGT TGTTGTCATT GTCGGCGCAA CTATCGGTAT CAAGCTGTTT AAGAAATTCA CCTCGAAAGC AAGCTGATAA ACCGATACAA TTAAAGGCTC CTTTTGGAGC CTTTTTTTTG GAGATTTTCA ACGTGAAAAA ATTATTATTC GCAATTCCTT TAGTTGTTCC TTTCTATTCT CACTCCGCTG AAACTGTTGA AAGTTGTTTA GCAAAATCCC ATACAGAAAA TTCATTTACT AACGTCTGGA AAGACGACAA AACTTTAGAT CGTTACGCTA ACTATGAGGG CTGTCTGTGG AATGCTACAG GCGTTGTAGT TTGTACTGGT GACGAAACTC AGTGTTACGG TACATGGGTT CCTATTGGGC TTGCTATCCC TGAAAATGAG GGTGGTGGCT CTGAGGGTGG CGGTTCTGAG GGTGGCGGTT CTGAGGGTGG CGGTACTAAA CCTCCTGAGT ACGGTGATAC ACCTATTCCG GGCTATACTT ATATCAACCC TCTCGACGGC ACTTATCCGC CTGGTACTGA GCAAAACCCC GCTAATCCTA ATCCTTCTCT TGAGGAGTCT CAGCCTCTTA ATACTTTCAT GTTTCAGAAT AATAGGTTCC GAAATAGGCA GGGGGCATTA ACTGTTTATA CGGGCACTGT TACTCAAGGC ACTGACCCCG TTAAAACTTA TTACCAGTAC ACTCCTGTAT CATCAAAAGC CATGTATGAC GCTTACTGGA ACGGTAAATT CAGAGACTGC GCTTTCCATT CTGGCTTTAA TGAGGATTTA TTTGTTTGTG AATATCAAGG CCAATCGTCT GACCTGCCTC AACCTCCTGT CAATGCTGGC GGCGGCTCTG GTGGTGGTTC TGGTGGCGGC TCTGAGGGTG GTGGCTCTGA GGGTGGCGGT TCTGAGGGTG GCGGCTCTGA GGGAGGCGGT TCCGGTGGTG GCTCTGGTTC CGGTGATTTT GATTATGAAA AGATGGCAAA CGCTAATAAG GGGGCTATGA CCGAAAATGC CGATGAAAAC GCGCTACAGT CTGACGCTAA AGGCAAACTT GATTCTGTCG CTACTGATTA CGGTGCTGCT ATCGATGGTT TCATTGGTGA CGTTTCCGGC CTTGCTAATG GTAATGGTGC TACTGGTGAT TTTGCTGGCT CTAATTCCCA AATGGCTCAA GTCGGTGACG GTGATAATTC ACCTTTAATG AATAATTTCC GTCAATATTT ACCTTCCCTC CCTCAATCGG TTGAATGTCG CCCTTTTGTC TTTGGCGCTG GTAAACCATA TGAATTTTCT ATTGATTGTG ACAAAATAAA CTTATTCCGT GGTGTCTTTG CGTTTCTTTT ATATGTTGCC ACCTTTATGT ATGTATTTTC TACGTTTGCT AACATACTGC GTAATAAGGA GTCTTAATCA TGCCAGTTCT TTTGGGTATT CCGTTATTAT TGCGTTTCCT CGGTTTCCTT CTGGTAACTT TGTTCGGCTA TCTGCTTACT TTTCTTAAAA AGGGCTTCGG TAAGATAGCT ATTGCTATTT CATTGTTTCT TGCTCTTATT ATTGGGCTTA ACTCAATTCT TGTGGGTTAT CTCTCTGATA TTAGCGCTCA ATTACCCTCT GACTTTGTTC AGGGTGTTCA GTTAATTCTC CCGTCTAATG CGCTTCCCTG TTTTTATGTT ATTCTCTCTG TAAAGGCTGC TATTTTCATT TTTGACGTTA AACAAAAAAT CGTTTCTTAT TTGGATTGGG ATAAATAATA TGGCTGTTTA TTTTGTAACT GGCAAATTAG GCTCTGGAAA GACGCTCGTT AGCGTTGGTA AGATTCAGGA TAAAATTGTA GCTGGGTGCA AAATAGCAAC TAATCTTGAT TTAAGGCTTC AAAACCTCCC GCAAGTCGGG AGGTTCGCTA AAACGCCTCG CGTTCTTAGA ATACCGGATA AGCCTTCTAT ATCTGATTTG CTTGCTATTG GGCGCGGTAA TGATTCCTAC GATGAAAATA AAAACGGCTT GCTTGTTCTC GATGAGTGCG GTACTTGGTT TAATACCCGT TCTTGGAATG ATAAGGAAAG ACAGCCGATT ATTGATTGGT TTCTACATGC TCGTAAATTA GGATGGGATA TTATTTTTCT TGTTCAGGAC TTATCTATTG TTGATAAACA GGCGCGTTCT GCATTAGCTG AACATGTTGT TTATTGTCGT CGTCTGGACA GAATTACTTT ACCTTTTGTC GGTACTTTAT ATTCTCTTAT TACTGGCTCG AAAATGCCTC TGCCTAAATT ACATGTTGGC GTTGTTAAAT ATGGCGATTC TCAATTAAGC CCTACTGTTG AGCGTTGGCT TTATACTGGT AAGAATTTGT ATAACGCATA TGATACTAAA CAGGCTTTTT CTAGTAATTA TGATTCCGGT GTTTATTCTT ATTTAACGCC TTATTTATCA CACGGTCGGT ATTTCAAACC ATTAAATTTA GGTCAGAAGA TGAAATTAAC TAAAATATAT TTGAAAAAGT TTTCTCGCGT TCTTTGTCTT GCGATTGGAT TTGCATCAGC ATTTACATAT AGTTATATAA CCCAACCTAA GCCGGAGGTT AAAAAGGTAG TCTCTCAGAC CTATGATTTT GATAAATTCA CTATTGACTC TTCTCAGCGT CTTAATCTAA GCTATCGCTA TGTTTTCAAG GATTCTAAGG GAAAATTAAT TAATAGCGAC GATTTACAGA AGCAAGGTTA TTCACTCACA TATATTGATT TATGTACTGT TTCCATTAAA AAAGGTAATT CAAATGAAAT TGTTAAATGT AATTAATTTT GTTTTCTTGA TGTTTGTTTC ATCATCTTCT TTTGCTCAGG TAATTGAAAT GAATAATTCG CCTCTGCGCG ATTTTGTAAC TTGGTATTCA AAGCAATCAG GCGAATCCGT TATTGTTTCT CCCGATGTAA AAGGTACTGT TACTGTATAT TCATCTGACG TTAAACCTGA AAATCTACGC AATTTCTTTA TTTCTGTTTT ACGTGCAAAT AATTTTGATA TGGTAGGTTC TAACCCTTCC ATTATTCAGA AGTATAATCC AAACAATCAG GATTATATTG ATGAATTGCC ATCATCTGAT AATCAGGAAT ATGATGATAA TTCCGCTCCT TCTGGTGGTT TCTTTGTTCC GCAAAATGAT AATGTTACTC AAACTTTTAA AATTAATAAC GTTCGGGCAA AGGATTTAAT ACGAGTTGTC GAATTGTTTG TAAAGTCTAA TACTTCTAAA TCCTCAAATG TATTATCTAT TGACGGCTCT AATCTATTAG TTGTTAGTGC TCCTAAAGAT ATTTTAGATA ACCTTCCTCA ATTCCTTTCA ACTGTTGATT TGCCAACTGA CCAGATATTG ATTGAGGGTT TGATATTTGA GGTTCAGCAA GGTGATGCTT TAGATTTTTC ATTTGCTGCT GGCTCTCAGC GTGGCACTGT TGCAGGCGGT GTTAATACTG ACCGCCTCAC CTCTGTTTTA TCTTCTGCTG GTGGTTCGTT CGGTATTTTT AATGGCGATG TTTTAGGGCT ATCAGTTCGC GCATTAAAGA CTAATAGCCA TTCAAAAATA TTGTCTGTGC CACGTATTCT TACGCTTTCA GGTCAGAAGG GTTCTATCTC TGTTGGCCAG AATGTCCCTT TTATTACTGG TCGTGTGACT GGTGAATCTG CCAATGTAAA TAATCCATTT CAGACGATTG AGCGTCAAAA TGTAGGTATT TCCATGAGCG TTTTTCCTGT TGCAATGGCT GGCGGTAATA TTGTTCTGGA TATTACCAGC AAGGCCGATA GTTTGAGTTC TTCTACTCAG GCAAGTGATG TTATTACTAA TCAAAGAAGT ATTGCTACAA CGGTTAATTT GCGTGATGGA CAGACTCTTT TACTCGGTGG CCTCACTGAT TATAAAAACA CTTCTCAGGA TTCTGGCGTA CCGTTCCTGT CTAAAATCCC TTTAATCGGC CTCCTGTTTA GCTCCCGCTC TGATTCTAAC GAGGAAAGCA CGTTATACGT GCTCGTCAAA GCAACCATAG TACGCGCCCT GTAGCGGCGC ATTAAGCGCG GCGGGTGTGG TGGTTACGCG CAGCGTGACC GCTACACTTG CCAGCGCCCT AGCGCCCGCT CCTTTCGCTT TCTTCCCTTC CTTTCTCGCC ACGTTCGCCG GCTTTCCCCG TCAAGCTCTA AATCGGGGGC TCCCTTTAGG GTTCCGATTT AGTGCTTTAC GGCACCTCGA CCCCAAAAAA CTTGATTTGG GTGATGGTTC ACGTAGTGGG CCATCGCCC

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Macromolecule #2: synthetic DNA segments

MacromoleculeName: synthetic DNA segments / type: dna / ID: 2 / Name.synonym: staple strands
Details: 163 smaller DNA segments with the following sequences: CAAAGGGCGGGTGCCTCGCTCACTGCTTAATGTTGCATGCGGTCACGTTG ATTGTTGTTCCGGCCAACCAGGGTGGTGCCAAGCGACAGGAAGCCGGA ...Details: 163 smaller DNA segments with the following sequences: CAAAGGGCGGGTGCCTCGCTCACTGCTTAATGTTGCATGCGGTCACGTTG ATTGTTGTTCCGGCCAACCAGGGTGGTGCCAAGCGACAGGAAGCCGGA TTTTTTTTTTGGGTGAGACGGGCGAGTTTTTTTTTTAAAGGGTCGTGCCGAGGATCCCCGGGTTTTT AGCGAAATCGCCTGGCCCTTGCCCCAGAGTAAAATAACATCACTT AAAATCAGCCCCCGGCAGGCGAAAATCCTGACGCTGGTTGAGAGAGGG GGGCCGTAAAGCACTAAATTTTTTTTTTTCGGAACCGGAAAGCCGGCGATTTTT TTTTTAGCGGTCCTTTTTTTTTTTTTGATGGTGGTTCAATAGCCCTTGGGC TTTTTACGTGGCAACAGCTGAGAAGTTTTCCTTTTTTTTTTCAGTCACGACGTTGT GCGCGCGGGGACGTGCTTCGCCGCTACAGCTTTCAATAGGAATTGCGG AGGCGGTTTTTTTTTTTTTGCGTAGAGTTTTTTTTTTATAGGGTTGAGTAAAGAACTT AACCTAAGGGTTTTTTTTTTAAGAAAGCGAAAGGTCACGCTAGCTCTTTTTTTTTTGAATTCGTAAT GCGTTGAATGAGTGTAAAGTGTAATTGTTAAGGAAGATGATAATCATG AACCCGCCGCGCCCGCTTTAATGAATCAGTTTGGCCTTATAAATCAAA TTTAACTCGCGTCTTTTTTTTTTTGAAATGGATCACCATCAACTGTTTTTTTTTTATAGCAAACAT CAAAACGTTAAAACTAGCTTGAGAGATCTGGAGCTCATTGAATCCCCCTCGAATCG ACTCTAAGCTGCATTCCAGTCGCGTGAACCGTCTATCAGGGCGATGTTTTTTTTTTGCCCACTAGGA TTTTTTACCGGCGCGTAAACAACCCGAAATTTTTTAAAAATTCTGAGT CAGTGTAGCGGAGCGGGCGCTAGGGCGAAAAACCAACAAGAGTCCACT ATTTTATCCTCGTTCGTGCATCTGGTGTAGCACCAGCACTCAGAGCAA TTTTTAACCAGAGGAATTTTTTTTTTAAACGCTCCATCACCTCATTAG GAGTAGAAGGTTGGGTAACGCCTTTTTTTTTTAGGGTGTTTTTATCCA TCTTTGATTAGTAAGAGTCTGTGGGCGATCCCAGGCAACAATAACCCA GCTGGCAGCTTTCGCGCGAGCAACACCGCTCCTGATTTAGAACCTGA ATTACGAATCAGTGCAGAATCCTGATTGCCTTCACCAGGTCGAGGTATCACCCAAATCAAGTTTTTT TTTTTGCAACGCTAGTTTGACATATCTTTTTTTTTTTGGTCAGTTGGCACCG GCGATTAATAGCTCAACTGGAAGTCTTTTGATCTATTATACCATCCTAGTCCTG GCTGGTAATATCCGAATTGAGCCAATTCTAGGTCAGGAAAAAGATGC ATCGGCCGGCGGATTCAGTATTGGCAAAGAGATGATGATTAACAATAA GACTTCTGGTCGGTACGCAGGCCACCATTTAGAGCTTGACGGCTAAAG CCAGTTCTGAGAGCTGTTTAGCATTGCATCATTAGAGAAA GCCGAAAGGGTACGGTGTCATGTTTTGCGGATGGCTTAGAGCTT AAGGTGCGGGGTTGATTCGAAGGTTACTTTAGGAGCACTAACGTTTTA TTAGGAGGCCCAAATTAACCGTTTTTTTTTTTTGCAGCCATTTTTTT AATGTGATGGGATACTGCAGGTACGGCCAGTTTTTCTTCTTCACCGGC CAACATAATAAAGCGAAGATAATTGCACGTGATGATGGCATCGGAAGT GCCAGGGCGCCGGAAGCAAGCTAACTTTTTTTTTTTCACATTAAGTGTTTTTTTTTTGACTCCAACGT TTTTTTCAATCGTTGTACCAACCTAATTTTTTTTTTAACATCGCCATTAAGATTTTCGAGCGG GTTGGTCATAGCTGTTTCCTGTGTGAAAAGCCTGTTTTAACCAT TATAAGCAAAAGGGGAAGCCTTTTTTTAATATTTCAATCATATGCGGG ACAAAATAATATACGAGCGTACTATGGTTTTTTTTTTTTGCTTTTGACGCTTTTT CCATCACCAAAAACTCCGCTCACAATTCCACACTTTTTTT GGCCAACAGATACGTGGTAATGCCGGGGAAGAAGG CGATTAGTCTTTAATTTTTTTTTTTGCGCGAATATGATAACGGAACTGACGAGAAACACCAGTCAATA CTATTTATGTCAATCCCTTCTGAAACAAGAGAATCGATCCTGAG ATAAATCACAGACACCACATTCAACTAATGAT TTTTTGGTCATTGGAATTTTTTTTTTCGGTAATCGTAATATTTTGTGCAATGCTT AGTCTACAAAAAGAACTGTTGTGAATTACCTTATAGAAATTTTT TTTTTGAATGGCTACCAGTAAATTGGCAGATTCACCATTTTTTTTTTGTCACA TAGAACAATTACATAACAAACAATCATAATAGTACCGACAAAA GATGAGAAAGGTAAATTGAAATCTACAAAAGAAGAGCAACACTATCAT TATGTGAGTGAAGTTACAAGCCAACGATTTAACATAAATTGTAA AATTATTTTTTTTTTAAATTCGCATTTCGGATTCACAGGCAATAGCATTAGG AATTTAATCAGCTCATTAAATGTTTAATAAATATAAAGGAAT TTTTTTAAATCATTCCTTTTTTTTTTGTGGGAACAAACTCAGGAAAATAGTAGTGAAAA GGTACCCTGAAAGAGGTCTAAACCAATTATTTTTTTTTTAATCAAGAT AATGGTAGCGCCATATCGTAACAGAATCAGCACGTATAAG ATAGACTTCAACCAGACCACCGCGCCTCCGGTATCTAACGAGCGTCT GCAACATGAGGCGGTGACCGTAAGCGAGTACCACCA GCAGCAGATTATCAAAAACAGATAGGCAGATTATACAAGACCTAAACTATATGTATCAATAG CAAATATTTTTTTTTTTTTCAAACCCTCAATCATGCTGAACACCAGAAGAGGTTTAAAT GAAAGAGAACAATGTTGGGAACCATCACGGATTAAAGTTGCAGCATTTTT ATTTTTTTTTTTTTAAATATGCTTTTTTTTTTAACTAAAGGGATTTTTTTTTTTGTGCTGCAAG TTGCTCTTCATTCCCATTTGGGCGGCACCGCGACGACAGTAAAACGCG TCAATAGATAATAAAGGCTTACAATAGCAGCGAATAAACAGCTTGATAATAAGTA TTTGAGTCGAGCTTCAAAGCGAAATATCGCCTGAGGCTACTAAAGAAG AACTTTTTTTTTTAATTCGACAACTTTTAAAACATCGC ATCAAAGCGGTATATTTTATATAACACCTCTTCGCTATCGGCCTTGCCT AACTTTGAGGTGCAGGGATTTCTTAATAATTTTTAAAGTCAGATTTAT TTTTTAAAATCAGGTCTTTGGCATCATTTTTTTTTTATTCTACTGATTTTTTTTTTTCGCACTCCA CCCGAAACATTTCGGTAGATTTGCGCAACTATTACCGCTAGCAATACT CGAACGTTATTAATCGTATTATAAACAACTGAATTTTGTCGTCTTTCCAGACG GTTTTTTTTTTTTTGAGTAACATTTACCTTTTGAGGCG TTATTCGGAAACAGTTAGATTAAGACGCTGTTATATAATTTAATGGGG AAGGGTGTTTGGATATAGATAAATTTACGAGCATGTTTTTTTTTTTAGAAACCAATCAACGGGTAT CATATCCAAAAGAAATTAGCAACGCAAGGAGTTAAATCTAAATT AGATCATTTTTTTCCATTACGCATAACGACAATGTAGAAAGGAG ACATTTTTTTTTTTCGGGAGAAACTCATTACCGTAATCTTGACAAGAACTGACCTTGTACAG CTTGAGATGGTTTAAATTACCTTATTTCAAAATTAAGCTA TTTTTACGAGACAAAATTCCTCATATTTTTTTTTTTATTTTA AAAACGAGTAGCCGGAGAGTTCTAGCGAAAAGCCTAAAAGGGACATTCT TATGACCCTGAAATCGGTCTGGCCTTACCTACATTTGACGAGAGCGGGAGCTATTTTT TAACCTTCCCTTAGAATCCTTGCCAATCGCATATTTTAAGTACC AATCGTCCGGATATAATAACGGACTGACCAGACGGTCAGTTACT CAATTTTTTTTTTATCAACGTAACAAAGCTGCTCATTCAGTA CTTTAAACTTTTTTTTTTAGTTCGCGATTTTGGCTATCATTTTT ACGCCAACCTGAAAGCGTAAGAAGATAGAACATATGTACCCCGGTTTG TTTTTAGGTAGAAAGATTCATCAGTACCAGACGACGATTTTTTTTTTTAAAAAC CAAAATAGCGAGAGGCTTTTGCGTTAATAATAGGAATAATA TCGACTGGATAGCGTCCATTTTTTTTTTATACTGCGAAATG TACGAGGCCAGATACAAGGACGTTGAGAGGGTTAAAGATTCAAATATTAGCTCATTGCTGGC AGTAAGTTTTGCCAGAGGGGGTAATAGTAATACCAGTCTA AACCCTCGTTTTGAGATTAACGAACTATTCAACCCAGTCAAATTATTT TTTATCAAAATCATAGGTCTTTTTTTTTTTGAGAGACTACCTATAAGG GTTTTAGTATTACCTGAGAAAATTATAACAGAGGGTGCCACGTGAGGG AACATACAGTATAAAAATCGCGAATTGCGTAAAATACCATCTAAAGATGGAAATTCGCCA TAATTTTGCTTCTGTGAATAAGGCTTGCCCAACATTATTACTTTTT GAACGCGATAGGCTGGCGCTATTAGGAACCGAATTCGCCTGAATATACAGTAAC CGAACGCAATAAGTTACCTTTGGGAATTAGAGCCTTAGCGTTTGCCATTTTT CGAAAGCCTGCAATAGTGTTCATTTGATTTCAACTGTGTAGGAG ACTGATATAAGTATATTTTTTTTTTGCCCGGAATAGGTAGGCTGAGTTTTT GATCAAGAAAAATGATTTTTTTTTTCCATATGAATAATACATCCAATTTTT ATATAATACTAGAATGTGATAATTTTAACCCAAAGACAAAATTTTTTTTTTGGGACCGACTTGAGTTTTT CATTTTAAAGTACACAGCGATTCCCATGTATACCGAAGCCCTTTTTGA GTAATTAATAAAGACAGAGGCGATAAAGCTTAATACTTCG CGCCATCTCAACAGTTTCAAATAAGACAAAAAGACACCACGGAATAAT CAACTTTGAAAGAGGTTTTTTTTTTACAGATGAACGGTCATCAAGA GGTAAAGTAATTCGCTAATGCAGAACGCGCCTTTTTTTTTTTGTTTATCAACATATACTTCAATCATTTTT TAACGAAGGCACAGCCCTCATAGTTTTTTTTTTTTAGCCCCACAAG GAATACGTACAAACAGCAAGAAACAATGAACCCTGAACTCACGTTGTA AGGCAAGTCGAAATGAGGTTTAGCGGATAATAGCGGGGGAAACGCA AACGAACTTTTTCAAATTGAGACGTCAGATGATTGCTTTGAATACCAA AACATGTTCATGTCCAGACTCATTTTAATAACGGTCACCGTCCGACATTC CACCCTGTATCGGTAGGCTCCATTAGACGGTGTTTAACGTCAAAAATG GGGATCCGAGGGTATTGACCCCACGGAGATCCCTCA TTTAAGAGGAATATTCCTAATGAAAAGAACGAACATGGGCGCCCTGTA GATATAGATTTTGCAATCCTTTGATTTAGAAGTATTAGACTTTACATTAGTA CCAAACGGGTAAAATTTTTTTTTTTACGTAATGCCACTGCCGGAAC GGTGAAGTTAAAGGGAATCATTGGAAGCAAGATTAGAGAATCAACAGTT GCGTACCTTTTGAAATATTCTAAATATAATGCTGAACTCAAACT GCCGTTGAACCTCCCAGCTACAATTTTATCCGATTTTTGAGAATTAAC GAAGCCGTACCGCATTCCAAGAATAATCGGTAAGCAGATAGCCTTTTT GCTTTATTTTCAAAAAAATTATCAGCAGCTATCTCCGTAACACTGAGT AATTTCAACAGTTTCTTTTTTTTTTAGCGGAGTGAGAAACAACAAC TAGCAGCCTTTACAGTTTTTTTTTTAGAGAATAACATA CCAACGTCTAAGAACGCGAGGCAACTAATAACTCCAACGCGAACGACA TTCGCCATATTAGGGTAATTGAGCGCTTAAGCCCAATACCGATAA AAAATAGTTGCTATCCTTATCACTCATCGAATAATATCGTCAGAAGCAATATAACT CCCAATCCAAATAAGAAACTGAATCTAAAATCTCCATCGTAGCCGCTT CACAGAGCCTAAGGAATTAGCAAATCTTCGGTCGGTTTTAATAAGAAACCCT AAAACAGGAAGAAAAGCTGTCTTTATAAACAACAAGAAAATAATAAGAAC AGCGCAAAAGGAGCTTTGCACCCGACTTGCGGGAGGTTTTAATTGCAA TGAACAATAGCAATTTGCTTTCACTCATCTGCAACGGCAT AGATAAGTAACTTTTTTTTTTGATCTAAAGTTTTAGTTACAAAATAAA AATTGAGTAATATCAGAACAACTAAATTTGCCCTGTATGGAGATATAGCA TTTTTGAACACAGGGATAGCAAGCCCCCACCACCCGACGACAACCGAC TTAACCGCCATTGTATCACATCTTCTATTCTTACGCGATAGCTACATA CAACGCCTGTAGCAGTACTCAGCCGCGACCGAAAACTTTAGGGCTTAT GATAAGACTCATAGACGGATATTCATGAGCCGCCGCCAGCATCGCCTC CATGATACCGCCACGCACCATTACCATTAGTTTCATCGTAAACAGTGT AGGTACCGCCACCAATGAAACCATCGAAGTTTGCCCTATT GCCGTCGAGAGGGTCAGGCGCATGCTCCATATCATAAGTGAGGAAGGCGGAACAGCC TTTTTACTCCTCAATTTTTTTTTTTTAAGCAGTAGCGACAGAATCATAGCAGCATTAGGATGT TTTTTCCAAGAAGGAATTTTTTTTTTACCGAGGATTAAATAAGAATTTTTTTTTTTAAACACCG ATGTGAATTAAATACCCAACCAGCGCTCCGGCTTAGGTTGGGAGAAGA TACCTCAGAGAATAGGAAATACCAAGCTTTAATTCAGCAGCGGAACAA GTCAAGGCCGCGTAGAAACTTATTACTTGTCACAAAATGCTGATGCAAATAA TTTTTTCTTTTCATAATCCCTTGATATTTTTTTTTTTTCACAAACAAATA TGCCTATTAGCAAAGAAACGTCACCCTCAGCGTCACCAACTAAAACGA ATGAGTGTACAGAGCCACTTTTTTTTTTCACCCTCAGAGCCG AAGTAGAGAAGGACCGTAATGTATCACCTTCCACAGACCAACCTAGTTGCGCCC GCCTTGTCAGAGCCGCCACCCTCAGAACCGACCAGAACCC AAACGATTGGAAAATCACGGTTGAGGAACCGATTGAGGGAGGTATGGT GAAAGCGCAGTCCGGGGTCATAATGCCCCACCACCAACATAAAGGTGGCA CATACATGGCTTTTTTTTTTTTTTGATGATACAGTCTGAAACATGA CCCCACCCTCTGGTAATAAGTTTTAATCTGAATTTCAGACTGTAGCGC CAGGTCAGACCGGAACTGACAGGACGGAACCACATTAAAGCACCAG CCAGTAACAGGAGCCACCTCCTCATTGGTCATAGCCCCCTTAAGCAAA TTAAAGAACTTTTGAAATCGCGAAACCGAGCCAGAAAGACAGCAATTC AAAATTCAGAAGGTAAAAATTATTTGCCCGTAGCATTTTCAAAGCCAGAATG ACAGTTTATTGCAGTATGGTTAATTTTCGCCTGAACGCCAACTACAGAGGTTATCATCAG ATAAAATTTTGCTCTTTCGGAACTTTAGCGTACCGTTCCAGTAAGCGT
Classification: DNA / Structure: SINGLE STRANDED / Synthetic?: Yes
Source (natural)Organism: synthetic construct (others)
Molecular weightExperimental: 2.4 MDa / Theoretical: 2.4 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration48 mg/mL
BufferpH: 7.6 / Details: 10 mM TRIS-HCl, 20 mM MgCl2, 5 mM NaCl, 1 mM EDTA
GridDetails: glow-discharged holey carbon grids with an ultrathin carbon film on top (Agar Scientific, catalog no. S187-4)
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 39436 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 4.41 µm / Nominal defocus min: 0.82 µm / Nominal magnification: 31000
Sample stageSpecimen holder model: OTHER
TemperatureMin: 80 K / Max: 90 K / Average: 85 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 39,000 times magnification
Legacy - Electron beam tilt params: 0
DateApr 1, 2012
Image recordingCategory: CCD / Film or detector model: FEI FALCON I (4k x 4k) / Digitization - Sampling interval: 14 µm / Number real images: 283 / Average electron dose: 10 e/Å2
Details: Every image is the average of sixteen frames recorded by the direct electron detector
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: each image
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 11.5 Å / Resolution method: OTHER / Software - Name: CTFFIND3, RELION
Details: RELION (= FREALIGN = XMIPP = 3DEM-convention). The final map is a composite map, which consists of maps filtered at different resolutions ranging from 14A at the periphery to 9A at the core ...Details: RELION (= FREALIGN = XMIPP = 3DEM-convention). The final map is a composite map, which consists of maps filtered at different resolutions ranging from 14A at the periphery to 9A at the core of the object. See publication for more details.
Number images used: 28502
DetailsParticles were manually selected. CTF parameters were estimated using CTFFIND3. An initial model was obtained by DNA origami structure prediction software, and the refinement was performed using the 3D auto-refine option in RELION.

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