4V5X

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Cryo-Em Structure of a 3D DNA-Origami Object.

Bai, X.Martin, T.G.Scheres, S.H.W.Dietz, H.

(2012) Proc.Natl.Acad.Sci.USA 109: 20012

  • DOI: 10.1073/pnas.1215713109
  • Primary Citation of Related Structures:  2YMG, 2YMF, 2YMH, 2YMI, 2YMR

  • PubMed 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 shown potential for creating user-defined 3D scaffol ...

    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.


    Organizational Affiliation

    Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
SCAFFOLD STRANDAA4896Escherichia virus M13
Entity ID: 2
MoleculeChainsLengthOrganism
SCAFFOLD STRANDBA2353Escherichia virus M13
Entity ID: 3
MoleculeChainsLengthOrganism
STAPLE STRANDA055synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
STAPLE STRANDA144synthetic construct
Entity ID: 5
MoleculeChainsLengthOrganism
STAPLE STRANDA250synthetic construct
Entity ID: 6
MoleculeChainsLengthOrganism
STAPLE STRANDA340synthetic construct
Entity ID: 7
MoleculeChainsLengthOrganism
STAPLE STRANDA448synthetic construct
Entity ID: 8
MoleculeChainsLengthOrganism
STAPLE STRANDA548synthetic construct
Entity ID: 9
MoleculeChainsLengthOrganism
STAPLE STRANDA650synthetic construct
Entity ID: 10
MoleculeChainsLengthOrganism
STAPLE STRANDA748synthetic construct
Entity ID: 11
MoleculeChainsLengthOrganism
STAPLE STRANDA848synthetic construct
Entity ID: 12
MoleculeChainsLengthOrganism
STAPLE STRANDAB40synthetic construct
Entity ID: 13
MoleculeChainsLengthOrganism
STAPLE STRANDAC48synthetic construct
Entity ID: 14
MoleculeChainsLengthOrganism
STAPLE STRANDAD50synthetic construct
Entity ID: 15
MoleculeChainsLengthOrganism
STAPLE STRANDAE46synthetic construct
Entity ID: 16
MoleculeChainsLengthOrganism
STAPLE STRANDAF48synthetic construct
Entity ID: 17
MoleculeChainsLengthOrganism
STAPLE STRANDAG46synthetic construct
Entity ID: 18
MoleculeChainsLengthOrganism
STAPLE STRANDAH48synthetic construct
Entity ID: 19
MoleculeChainsLengthOrganism
STAPLE STRANDAI48synthetic construct
Entity ID: 20
MoleculeChainsLengthOrganism
STAPLE STRANDAJ52synthetic construct
Entity ID: 21
MoleculeChainsLengthOrganism
STAPLE STRANDAK60synthetic construct
Entity ID: 22
MoleculeChainsLengthOrganism
STAPLE STRANDAL48synthetic construct
Entity ID: 23
MoleculeChainsLengthOrganism
STAPLE STRANDAM50synthetic construct
Entity ID: 24
MoleculeChainsLengthOrganism
STAPLE STRANDAN48synthetic construct
Entity ID: 25
MoleculeChainsLengthOrganism
STAPLE STRANDAO48synthetic construct
Entity ID: 26
MoleculeChainsLengthOrganism
STAPLE STRANDAP40synthetic construct
Entity ID: 27
MoleculeChainsLengthOrganism
STAPLE STRANDAQ57synthetic construct
Entity ID: 28
MoleculeChainsLengthOrganism
STAPLE STRANDAR63synthetic construct
Entity ID: 29
MoleculeChainsLengthOrganism
STAPLE STRANDAS64synthetic construct
Entity ID: 30
MoleculeChainsLengthOrganism
STAPLE STRANDAT48synthetic construct
Entity ID: 31
MoleculeChainsLengthOrganism
STAPLE STRANDAU48synthetic construct
Entity ID: 32
MoleculeChainsLengthOrganism
STAPLE STRANDAV52synthetic construct
Entity ID: 33
MoleculeChainsLengthOrganism
STAPLE STRANDAW50synthetic construct
Entity ID: 34
MoleculeChainsLengthOrganism
STAPLE STRANDAX48synthetic construct
Entity ID: 35
MoleculeChainsLengthOrganism
STAPLE STRANDAY42synthetic construct
Entity ID: 36
MoleculeChainsLengthOrganism
STAPLE STRANDAZ54synthetic construct
Entity ID: 37
MoleculeChainsLengthOrganism
STAPLE STRANDAb45synthetic construct
Entity ID: 38
MoleculeChainsLengthOrganism
STAPLE STRANDAc70synthetic construct
Entity ID: 39
MoleculeChainsLengthOrganism
STAPLE STRANDAd48synthetic construct
Entity ID: 40
MoleculeChainsLengthOrganism
STAPLE STRANDAf48synthetic construct
Entity ID: 41
MoleculeChainsLengthOrganism
STAPLE STRANDAg48synthetic construct
Entity ID: 42
MoleculeChainsLengthOrganism
STAPLE STRANDAh44synthetic construct
Entity ID: 43
MoleculeChainsLengthOrganism
STAPLE STRANDAi46synthetic construct
Entity ID: 44
MoleculeChainsLengthOrganism
STAPLE STRANDAj62synthetic construct
Entity ID: 45
MoleculeChainsLengthOrganism
STAPLE STRANDAk46synthetic construct
Entity ID: 46
MoleculeChainsLengthOrganism
STAPLE STRANDAl48synthetic construct
Entity ID: 47
MoleculeChainsLengthOrganism
STAPLE STRANDAm48synthetic construct
Entity ID: 48
MoleculeChainsLengthOrganism
STAPLE STRANDAn48synthetic construct
Entity ID: 49
MoleculeChainsLengthOrganism
STAPLE STRANDAo36synthetic construct
Entity ID: 50
MoleculeChainsLengthOrganism
STAPLE STRANDAs48synthetic construct
Entity ID: 51
MoleculeChainsLengthOrganism
STAPLE STRANDAu48synthetic construct
Entity ID: 52
MoleculeChainsLengthOrganism
STAPLE STRANDAv48synthetic construct
Entity ID: 53
MoleculeChainsLengthOrganism
STAPLE STRANDAw48synthetic construct
Entity ID: 54
MoleculeChainsLengthOrganism
STAPLE STRANDAx52synthetic construct
Entity ID: 55
MoleculeChainsLengthOrganism
STAPLE STRANDAy38synthetic construct
Entity ID: 56
MoleculeChainsLengthOrganism
STAPLE STRANDAz51synthetic construct
Entity ID: 57
MoleculeChainsLengthOrganism
STAPLE STRANDB048synthetic construct
Entity ID: 58
MoleculeChainsLengthOrganism
STAPLE STRANDB159synthetic construct
Entity ID: 59
MoleculeChainsLengthOrganism
STAPLE STRANDB236synthetic construct
Entity ID: 60
MoleculeChainsLengthOrganism
STAPLE STRANDB348synthetic construct
Entity ID: 61
MoleculeChainsLengthOrganism
STAPLE STRANDB448synthetic construct
Entity ID: 62
MoleculeChainsLengthOrganism
STAPLE STRANDB540synthetic construct
Entity ID: 63
MoleculeChainsLengthOrganism
STAPLE STRANDB650synthetic construct
Entity ID: 64
MoleculeChainsLengthOrganism
STAPLE STRANDB744synthetic construct
Entity ID: 65
MoleculeChainsLengthOrganism
STAPLE STRANDB840synthetic construct
Entity ID: 66
MoleculeChainsLengthOrganism
STAPLE STRANDB955synthetic construct
Entity ID: 67
MoleculeChainsLengthOrganism
STAPLE STRANDBB48synthetic construct
Entity ID: 68
MoleculeChainsLengthOrganism
STAPLE STRANDBC44synthetic construct
Entity ID: 69
MoleculeChainsLengthOrganism
STAPLE STRANDBD35synthetic construct
Entity ID: 70
MoleculeChainsLengthOrganism
STAPLE STRANDBE68synthetic construct
Entity ID: 71
MoleculeChainsLengthOrganism
STAPLE STRANDBF40synthetic construct
Entity ID: 72
MoleculeChainsLengthOrganism
STAPLE STRANDBG49synthetic construct
Entity ID: 73
MoleculeChainsLengthOrganism
STAPLE STRANDBH42synthetic construct
Entity ID: 74
MoleculeChainsLengthOrganism
STAPLE STRANDBI42synthetic construct
Entity ID: 75
MoleculeChainsLengthOrganism
STAPLE STRANDBJ58synthetic construct
Entity ID: 76
MoleculeChainsLengthOrganism
STAPLE STRANDBK44synthetic construct
Entity ID: 77
MoleculeChainsLengthOrganism
STAPLE STRANDBL48synthetic construct
Entity ID: 78
MoleculeChainsLengthOrganism
STAPLE STRANDBM52synthetic construct
Entity ID: 79
MoleculeChainsLengthOrganism
STAPLE STRANDBN63synthetic construct
Entity ID: 80
MoleculeChainsLengthOrganism
STAPLE STRANDBO49synthetic construct
Entity ID: 81
MoleculeChainsLengthOrganism
STAPLE STRANDBP66synthetic construct
Entity ID: 82
MoleculeChainsLengthOrganism
STAPLE STRANDBQ48synthetic construct
Entity ID: 83
MoleculeChainsLengthOrganism
STAPLE STRANDBR64synthetic construct
Entity ID: 84
MoleculeChainsLengthOrganism
STAPLE STRANDBS48synthetic construct
Entity ID: 85
MoleculeChainsLengthOrganism
STAPLE STRANDBT52synthetic construct
Entity ID: 86
MoleculeChainsLengthOrganism
STAPLE STRANDBU55synthetic construct
Entity ID: 87
MoleculeChainsLengthOrganism
STAPLE STRANDBV44synthetic construct
Entity ID: 88
MoleculeChainsLengthOrganism
STAPLE STRANDBW53synthetic construct
Entity ID: 89
MoleculeChainsLengthOrganism
STAPLE STRANDBX48synthetic construct
Entity ID: 90
MoleculeChainsLengthOrganism
STAPLE STRANDBY48synthetic construct
Entity ID: 91
MoleculeChainsLengthOrganism
STAPLE STRANDBZ66synthetic construct
Entity ID: 92
MoleculeChainsLengthOrganism
STAPLE STRANDBa48synthetic construct
Entity ID: 93
MoleculeChainsLengthOrganism
STAPLE STRANDBb68synthetic construct
Entity ID: 94
MoleculeChainsLengthOrganism
STAPLE STRANDBc50synthetic construct
Entity ID: 95
MoleculeChainsLengthOrganism
STAPLE STRANDBd56synthetic construct
Entity ID: 96
MoleculeChainsLengthOrganism
STAPLE STRANDBe48synthetic construct
Entity ID: 97
MoleculeChainsLengthOrganism
STAPLE STRANDBf48synthetic construct
Entity ID: 98
MoleculeChainsLengthOrganism
STAPLE STRANDBg47synthetic construct
Entity ID: 99
MoleculeChainsLengthOrganism
STAPLE STRANDBh48synthetic construct
Entity ID: 100
MoleculeChainsLengthOrganism
STAPLE STRANDBi67synthetic construct
Entity ID: 101
MoleculeChainsLengthOrganism
STAPLE STRANDBj45synthetic construct
Entity ID: 102
MoleculeChainsLengthOrganism
STAPLE STRANDBk67synthetic construct
Entity ID: 103
MoleculeChainsLengthOrganism
STAPLE STRANDBl48synthetic construct
Entity ID: 104
MoleculeChainsLengthOrganism
STAPLE STRANDBm48synthetic construct
Entity ID: 105
MoleculeChainsLengthOrganism
STAPLE STRANDBn67synthetic construct
Entity ID: 106
MoleculeChainsLengthOrganism
STAPLE STRANDBo67synthetic construct
Entity ID: 107
MoleculeChainsLengthOrganism
STAPLE STRANDBp48synthetic construct
Entity ID: 108
MoleculeChainsLengthOrganism
STAPLE STRANDBq58synthetic construct
Entity ID: 109
MoleculeChainsLengthOrganism
STAPLE STRANDBr51synthetic construct
Entity ID: 110
MoleculeChainsLengthOrganism
STAPLE STRANDBs54synthetic construct
Entity ID: 111
MoleculeChainsLengthOrganism
STAPLE STRANDC041synthetic construct
Entity ID: 112
MoleculeChainsLengthOrganism
STAPLE STRANDC151synthetic construct
Entity ID: 113
MoleculeChainsLengthOrganism
STAPLE STRANDC256synthetic construct
Entity ID: 114
MoleculeChainsLengthOrganism
STAPLE STRANDC348synthetic construct
Entity ID: 115
MoleculeChainsLengthOrganism
STAPLE STRANDC471synthetic construct
Entity ID: 116
MoleculeChainsLengthOrganism
STAPLE STRANDC562synthetic construct
Entity ID: 117
MoleculeChainsLengthOrganism
STAPLE STRANDC648synthetic construct
Entity ID: 118
MoleculeChainsLengthOrganism
STAPLE STRANDC752synthetic construct
Entity ID: 119
MoleculeChainsLengthOrganism
STAPLE STRANDC844synthetic construct
Entity ID: 120
MoleculeChainsLengthOrganism
STAPLE STRANDCB54synthetic construct
Entity ID: 121
MoleculeChainsLengthOrganism
STAPLE STRANDCC47synthetic construct
Entity ID: 122
MoleculeChainsLengthOrganism
STAPLE STRANDCD48synthetic construct
Entity ID: 123
MoleculeChainsLengthOrganism
STAPLE STRANDCE40synthetic construct
Entity ID: 124
MoleculeChainsLengthOrganism
STAPLE STRANDCF40synthetic construct
Entity ID: 125
MoleculeChainsLengthOrganism
STAPLE STRANDCG44synthetic construct
Entity ID: 126
MoleculeChainsLengthOrganism
STAPLE STRANDCH48synthetic construct
Entity ID: 127
MoleculeChainsLengthOrganism
STAPLE STRANDCI44synthetic construct
Entity ID: 128
MoleculeChainsLengthOrganism
STAPLE STRANDCJ59synthetic construct
Entity ID: 129
MoleculeChainsLengthOrganism
STAPLE STRANDCK48synthetic construct
Entity ID: 130
MoleculeChainsLengthOrganism
STAPLE STRANDCL48synthetic construct
Entity ID: 131
MoleculeChainsLengthOrganism
STAPLE STRANDCM54synthetic construct
Entity ID: 132
MoleculeChainsLengthOrganism
STAPLE STRANDCN41synthetic construct
Entity ID: 133
MoleculeChainsLengthOrganism
STAPLE STRANDCO48synthetic construct
Entity ID: 134
MoleculeChainsLengthOrganism
STAPLE STRANDCP56synthetic construct
Entity ID: 135
MoleculeChainsLengthOrganism
STAPLE STRANDCQ38synthetic construct
Entity ID: 136
MoleculeChainsLengthOrganism
STAPLE STRANDCR48synthetic construct
Entity ID: 137
MoleculeChainsLengthOrganism
STAPLE STRANDCS48synthetic construct
Entity ID: 138
MoleculeChainsLengthOrganism
STAPLE STRANDCT48synthetic construct
Entity ID: 139
MoleculeChainsLengthOrganism
STAPLE STRANDCU32synthetic construct
Entity ID: 140
MoleculeChainsLengthOrganism
STAPLE STRANDCV53synthetic construct
Entity ID: 141
MoleculeChainsLengthOrganism
STAPLE STRANDCW38synthetic construct
Entity ID: 142
MoleculeChainsLengthOrganism
STAPLE STRANDCX47synthetic construct
Entity ID: 143
MoleculeChainsLengthOrganism
STAPLE STRANDCY43synthetic construct
Entity ID: 144
MoleculeChainsLengthOrganism
STAPLE STRANDCZ48synthetic construct
Entity ID: 145
MoleculeChainsLengthOrganism
STAPLE STRANDCb44synthetic construct
Entity ID: 146
MoleculeChainsLengthOrganism
STAPLE STRANDCc62synthetic construct
Entity ID: 147
MoleculeChainsLengthOrganism
STAPLE STRANDCd42synthetic construct
Entity ID: 148
MoleculeChainsLengthOrganism
STAPLE STRANDCe52synthetic construct
Entity ID: 149
MoleculeChainsLengthOrganism
STAPLE STRANDCf48synthetic construct
Entity ID: 150
MoleculeChainsLengthOrganism
STAPLE STRANDCg46synthetic construct
Entity ID: 151
MoleculeChainsLengthOrganism
STAPLE STRANDCh47synthetic construct
Entity ID: 152
MoleculeChainsLengthOrganism
STAPLE STRANDCk29synthetic construct
Entity ID: 153
MoleculeChainsLengthOrganism
STAPLE STRANDCp48synthetic construct
Entity ID: 154
MoleculeChainsLengthOrganism
STAPLE STRANDCq40synthetic construct
Entity ID: 155
MoleculeChainsLengthOrganism
STAPLE STRANDCr46synthetic construct
Entity ID: 156
MoleculeChainsLengthOrganism
STAPLE STRANDCs49synthetic construct
Entity ID: 157
MoleculeChainsLengthOrganism
STAPLE STRANDCt44synthetic construct
Entity ID: 158
MoleculeChainsLengthOrganism
STAPLE STRANDCu60synthetic construct
Entity ID: 159
MoleculeChainsLengthOrganism
STAPLE STRANDCv46synthetic construct
Entity ID: 160
MoleculeChainsLengthOrganism
STAPLE STRANDCw54synthetic construct
Entity ID: 161
MoleculeChainsLengthOrganism
STAPLE STRANDCx46synthetic construct
Entity ID: 162
MoleculeChainsLengthOrganism
STAPLE STRANDCy66synthetic construct
Entity ID: 163
MoleculeChainsLengthOrganism
STAPLE STRANDCz48synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Type: Other
  • Version 1.2: 2015-03-25
    Type: Other
  • Version 2.0: 2017-08-02
    Type: Advisory, Atomic model, Data collection, Derived calculations