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- PDB-7bho: DNA origami signpost designed model -

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Basic information

Entry
Database: PDB / ID: 7bho
TitleDNA origami signpost designed model
Components
  • (DNA) x 237
  • DNA scaffold
KeywordsDNA / Origami / Nanostructure / Signpost / SPOT
Function / homologyDNA / DNA (> 10) / DNA (> 100) / DNA (> 1000)
Function and homology information
Biological speciesEscherichia virus M13
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 36.44 Å
AuthorsSilvester, E. / Vollmer, B. / Prazak, V. / Vasishtan, D. / Machala, E.A. / Whittle, C. / Black, S. / Bath, J. / Turberfield, A.J. / Gruenewald, K. / Baker, L.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/R017875/1 United Kingdom
Wellcome Trust107806/A/15/Z United Kingdom
CitationJournal: Cell / Year: 2021
Title: DNA origami signposts for identifying proteins on cell membranes by electron cryotomography.
Authors: Emma Silvester / Benjamin Vollmer / Vojtěch Pražák / Daven Vasishtan / Emily A Machala / Catheryne Whittle / Susan Black / Jonathan Bath / Andrew J Turberfield / Kay Grünewald / Lindsay A Baker /
Abstract: Electron cryotomography (cryoET), an electron cryomicroscopy (cryoEM) modality, has changed our understanding of biological function by revealing the native molecular details of membranes, viruses, ...Electron cryotomography (cryoET), an electron cryomicroscopy (cryoEM) modality, has changed our understanding of biological function by revealing the native molecular details of membranes, viruses, and cells. However, identification of individual molecules within tomograms from cryoET is challenging because of sample crowding and low signal-to-noise ratios. Here, we present a tagging strategy for cryoET that precisely identifies individual protein complexes in tomograms without relying on metal clusters. Our method makes use of DNA origami to produce "molecular signposts" that target molecules of interest, here via fluorescent fusion proteins, providing a platform generally applicable to biological surfaces. We demonstrate the specificity of signpost origami tags (SPOTs) in vitro as well as their suitability for cryoET of membrane vesicles, enveloped viruses, and the exterior of intact mammalian cells.
History
DepositionJan 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1May 1, 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-12188
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A1: DNA
A2: DNA
A3: DNA
A4: DNA
A5: DNA
A6: DNA
A7: DNA
A8: DNA
A9: DNA
AA: DNA
AB: DNA scaffold
AC: DNA
AD: DNA
B1: DNA
B2: DNA
B3: DNA
B4: DNA
B5: DNA
B6: DNA
B7: DNA
B8: DNA
B9: DNA
BA: DNA
BC: DNA
BD: DNA
C1: DNA
C2: DNA
C3: DNA
C5: DNA
C6: DNA
C7: DNA
C8: DNA
C9: DNA
CA: DNA
CC: DNA
CD: DNA
D1: DNA
D2: DNA
D3: DNA
D5: DNA
D6: DNA
D7: DNA
D8: DNA
D9: DNA
DA: DNA
DC: DNA
DD: DNA
E1: DNA
E2: DNA
E3: DNA
E5: DNA
E6: DNA
E7: DNA
E8: DNA
E9: DNA
EA: DNA
EC: DNA
ED: DNA
F1: DNA
F2: DNA
F3: DNA
F5: DNA
F6: DNA
F7: DNA
F8: DNA
F9: DNA
FA: DNA
FC: DNA
FD: DNA
G1: DNA
G2: DNA
G3: DNA
G5: DNA
G6: DNA
G7: DNA
G8: DNA
G9: DNA
GA: DNA
GC: DNA
GD: DNA
H1: DNA
H2: DNA
H3: DNA
H5: DNA
H6: DNA
H7: DNA
H8: DNA
H9: DNA
HA: DNA
HC: DNA
HD: DNA
I1: DNA
I2: DNA
I3: DNA
I5: DNA
I6: DNA
I7: DNA
I8: DNA
I9: DNA
IA: DNA
IC: DNA
ID: DNA
J1: DNA
J2: DNA
J3: DNA
J5: DNA
J6: DNA
J7: DNA
J8: DNA
J9: DNA
JA: DNA
JC: DNA
JD: DNA
K1: DNA
K2: DNA
K3: DNA
K5: DNA
K6: DNA
K7: DNA
K8: DNA
K9: DNA
KA: DNA
KC: DNA
KD: DNA
L1: DNA
L2: DNA
L3: DNA
L5: DNA
L6: DNA
L7: DNA
L8: DNA
L9: DNA
LA: DNA
LC: DNA
LD: DNA
M2: DNA
M3: DNA
M5: DNA
M6: DNA
M7: DNA
M8: DNA
M9: DNA
MA: DNA
MC: DNA
MD: DNA
N2: DNA
N3: DNA
N5: DNA
N6: DNA
N7: DNA
N8: DNA
N9: DNA
NA: DNA
NC: DNA
ND: DNA
O2: DNA
O3: DNA
O5: DNA
O6: DNA
O7: DNA
O8: DNA
O9: DNA
OA: DNA
OC: DNA
OD: DNA
P2: DNA
P3: DNA
P5: DNA
P6: DNA
P7: DNA
P8: DNA
P9: DNA
PA: DNA
PC: DNA
PD: DNA
Q2: DNA
Q3: DNA
Q5: DNA
Q7: DNA
Q8: DNA
Q9: DNA
QA: DNA
QC: DNA
QD: DNA
R2: DNA
R3: DNA
R5: DNA
R7: DNA
R8: DNA
R9: DNA
RA: DNA
RC: DNA
RD: DNA
S2: DNA
S3: DNA
S5: DNA
S7: DNA
S8: DNA
S9: DNA
SA: DNA
SC: DNA
SD: DNA
T2: DNA
T3: DNA
T5: DNA
T7: DNA
T8: DNA
T9: DNA
TA: DNA
TC: DNA
TD: DNA
U2: DNA
U3: DNA
U5: DNA
U7: DNA
U8: DNA
U9: DNA
UA: DNA
UC: DNA
UD: DNA
V2: DNA
V3: DNA
V5: DNA
V7: DNA
V8: DNA
V9: DNA
VA: DNA
VC: DNA
VD: DNA
W3: DNA
W5: DNA
W7: DNA
W8: DNA
W9: DNA
WD: DNA
X5: DNA
X7: DNA
X9: DNA


Theoretical massNumber of molelcules
Total (without water)4,453,173238
Polymers4,453,173238
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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DNA chain , 238 types, 238 molecules A1A2A3A4A5A6A7A8A9AAABACADB1B2B3B4B5B6B7B8B9BABCBDC1C2C3C5C6...

#1: DNA chain DNA


Mass: 17493.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#2: DNA chain DNA


Mass: 9535.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#3: DNA chain DNA


Mass: 7080.585 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#4: DNA chain DNA


Mass: 8603.578 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#5: DNA chain DNA


Mass: 12941.319 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#6: DNA chain DNA


Mass: 8005.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#7: DNA chain DNA


Mass: 11353.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#8: DNA chain DNA


Mass: 7422.825 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#9: DNA chain DNA


Mass: 5904.841 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#10: DNA chain DNA


Mass: 7108.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#11: DNA chain DNA scaffold


Mass: 2236242.500 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#12: DNA chain DNA


Mass: 5530.603 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#13: DNA chain DNA


Mass: 12390.986 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#14: DNA chain DNA


Mass: 13070.442 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#15: DNA chain DNA


Mass: 5510.635 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#16: DNA chain DNA


Mass: 5609.662 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#17: DNA chain DNA


Mass: 5555.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#18: DNA chain DNA


Mass: 11687.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#19: DNA chain DNA


Mass: 7391.815 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#20: DNA chain DNA


Mass: 5442.528 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#21: DNA chain DNA


Mass: 8271.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#22: DNA chain DNA


Mass: 16751.752 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#23: DNA chain DNA


Mass: 9871.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#24: DNA chain DNA


Mass: 11491.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#25: DNA chain DNA


Mass: 5878.877 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#26: DNA chain DNA


Mass: 8194.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#27: DNA chain DNA


Mass: 5509.594 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#28: DNA chain DNA


Mass: 6586.274 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#29: DNA chain DNA


Mass: 13069.505 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#30: DNA chain DNA


Mass: 13944.970 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#31: DNA chain DNA


Mass: 10180.564 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#32: DNA chain DNA


Mass: 16720.738 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#33: DNA chain DNA


Mass: 8364.422 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#34: DNA chain DNA


Mass: 5851.834 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#35: DNA chain DNA


Mass: 9505.150 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#36: DNA chain DNA


Mass: 7987.166 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#37: DNA chain DNA


Mass: 12710.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#38: DNA chain DNA


Mass: 5504.584 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#39: DNA chain DNA


Mass: 10506.789 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#40: DNA chain DNA


Mass: 6494.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#41: DNA chain DNA


Mass: 14167.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#42: DNA chain DNA


Mass: 6528.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#43: DNA chain DNA


Mass: 14103.091 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#44: DNA chain DNA


Mass: 9275.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#45: DNA chain DNA


Mass: 7083.601 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#46: DNA chain DNA


Mass: 5516.579 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#47: DNA chain DNA


Mass: 12904.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#48: DNA chain DNA


Mass: 10093.514 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#49: DNA chain DNA


Mass: 13233.516 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#50: DNA chain DNA


Mass: 5845.838 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#51: DNA chain DNA


Mass: 9268.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#52: DNA chain DNA


Mass: 11219.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#53: DNA chain DNA


Mass: 7422.826 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#54: DNA chain DNA


Mass: 10027.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#55: DNA chain DNA


Mass: 12664.166 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#56: DNA chain DNA


Mass: 5842.767 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#57: DNA chain DNA


Mass: 7111.594 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#58: DNA chain DNA


Mass: 11687.541 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#59: DNA chain DNA


Mass: 6047.935 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#60: DNA chain DNA


Mass: 10732.911 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#61: DNA chain DNA


Mass: 8000.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#62: DNA chain DNA


Mass: 14625.446 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#63: DNA chain DNA


Mass: 5567.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#64: DNA chain DNA


Mass: 8940.809 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#65: DNA chain DNA


Mass: 5469.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#66: DNA chain DNA


Mass: 5573.644 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#67: DNA chain DNA


Mass: 10272.642 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#68: DNA chain DNA


Mass: 5892.847 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#69: DNA chain DNA


Mass: 14549.442 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#70: DNA chain DNA


Mass: 5813.787 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#71: DNA chain DNA


Mass: 5486.610 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#72: DNA chain DNA


Mass: 8571.525 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#73: DNA chain DNA


Mass: 7363.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#74: DNA chain DNA


Mass: 10174.567 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#75: DNA chain DNA


Mass: 8841.782 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#76: DNA chain DNA


Mass: 7259.697 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#77: DNA chain DNA


Mass: 5826.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#78: DNA chain DNA


Mass: 5893.835 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#79: DNA chain DNA


Mass: 8013.166 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#80: DNA chain DNA


Mass: 5589.642 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#81: DNA chain DNA


Mass: 5578.652 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#82: DNA chain DNA


Mass: 15620.033 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#83: DNA chain DNA


Mass: 12955.378 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#84: DNA chain DNA


Mass: 12223.852 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#85: DNA chain DNA


Mass: 10792.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#86: DNA chain DNA


Mass: 6189.014 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#87: DNA chain DNA


Mass: 6457.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#88: DNA chain DNA


Mass: 9627.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#89: DNA chain DNA


Mass: 9319.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#90: DNA chain DNA


Mass: 7309.723 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#91: DNA chain DNA


Mass: 7393.791 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#92: DNA chain DNA


Mass: 6520.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#93: DNA chain DNA


Mass: 15075.700 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#94: DNA chain DNA


Mass: 18312.771 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#95: DNA chain DNA


Mass: 13164.511 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#96: DNA chain DNA


Mass: 5776.743 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#97: DNA chain DNA


Mass: 9257.968 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#98: DNA chain DNA


Mass: 12352.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#99: DNA chain DNA


Mass: 9281.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#100: DNA chain DNA


Mass: 5796.800 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#101: DNA chain DNA


Mass: 7040.560 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#102: DNA chain DNA


Mass: 10313.655 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#103: DNA chain DNA


Mass: 8598.568 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#104: DNA chain DNA


Mass: 12807.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#105: DNA chain DNA


Mass: 9136.924 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#106: DNA chain DNA


Mass: 11491.426 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#107: DNA chain DNA


Mass: 13599.819 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#108: DNA chain DNA


Mass: 17327.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#109: DNA chain DNA


Mass: 16768.789 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#110: DNA chain DNA


Mass: 5485.569 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#111: DNA chain DNA


Mass: 5853.811 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#112: DNA chain DNA


Mass: 7970.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#113: DNA chain DNA


Mass: 11850.653 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#114: DNA chain DNA


Mass: 13884.996 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#115: DNA chain DNA


Mass: 10135.530 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#116: DNA chain DNA


Mass: 5518.608 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#117: DNA chain DNA


Mass: 14975.593 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#118: DNA chain DNA


Mass: 5481.564 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#119: DNA chain DNA


Mass: 13280.526 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#120: DNA chain DNA


Mass: 7049.573 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#121: DNA chain DNA


Mass: 7994.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#122: DNA chain DNA


Mass: 15682.107 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#123: DNA chain DNA


Mass: 7497.865 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#124: DNA chain DNA


Mass: 7072.612 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#125: DNA chain DNA


Mass: 17386.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#126: DNA chain DNA


Mass: 17187.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#127: DNA chain DNA


Mass: 5730.722 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#128: DNA chain DNA


Mass: 7016.535 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#129: DNA chain DNA


Mass: 7357.788 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#130: DNA chain DNA


Mass: 18570.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#131: DNA chain DNA


Mass: 7419.846 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#132: DNA chain DNA


Mass: 5860.849 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#133: DNA chain DNA


Mass: 6740.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#134: DNA chain DNA


Mass: 5510.582 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#135: DNA chain DNA


Mass: 5489.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#136: DNA chain DNA


Mass: 6468.194 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#137: DNA chain DNA


Mass: 10808.056 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#138: DNA chain DNA


Mass: 12895.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#139: DNA chain DNA


Mass: 7581.916 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#140: DNA chain DNA


Mass: 7942.187 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#141: DNA chain DNA


Mass: 7929.166 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#142: DNA chain DNA


Mass: 7086.634 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#143: DNA chain DNA


Mass: 13427.625 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#144: DNA chain DNA


Mass: 7140.574 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#145: DNA chain DNA


Mass: 17786.482 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#146: DNA chain DNA


Mass: 7395.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#147: DNA chain DNA


Mass: 10693.874 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#148: DNA chain DNA


Mass: 9609.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#149: DNA chain DNA


Mass: 15608.057 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#150: DNA chain DNA


Mass: 7091.574 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#151: DNA chain DNA


Mass: 6408.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#152: DNA chain DNA


Mass: 16241.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#153: DNA chain DNA


Mass: 5936.877 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#154: DNA chain DNA


Mass: 11725.536 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#155: DNA chain DNA


Mass: 6246.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#156: DNA chain DNA


Mass: 18417.836 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#157: DNA chain DNA


Mass: 7458.882 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#158: DNA chain DNA


Mass: 15099.775 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#159: DNA chain DNA


Mass: 7055.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#160: DNA chain DNA


Mass: 16095.363 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#161: DNA chain DNA


Mass: 17841.516 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#162: DNA chain DNA


Mass: 5461.597 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#163: DNA chain DNA


Mass: 5806.802 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#164: DNA chain DNA


Mass: 7219.672 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#165: DNA chain DNA


Mass: 17933.645 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#166: DNA chain DNA


Mass: 9452.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#167: DNA chain DNA


Mass: 11567.469 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#168: DNA chain DNA


Mass: 5516.579 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#169: DNA chain DNA


Mass: 5566.605 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#170: DNA chain DNA


Mass: 5531.644 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#171: DNA chain DNA


Mass: 7210.674 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#172: DNA chain DNA


Mass: 7307.708 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#173: DNA chain DNA


Mass: 11712.607 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#174: DNA chain DNA


Mass: 7121.596 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#175: DNA chain DNA


Mass: 7067.603 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#176: DNA chain DNA


Mass: 5828.852 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#177: DNA chain DNA


Mass: 7045.569 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#178: DNA chain DNA


Mass: 12911.297 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#179: DNA chain DNA


Mass: 7064.585 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#180: DNA chain DNA


Mass: 7313.743 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#181: DNA chain DNA


Mass: 11899.710 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#182: DNA chain DNA


Mass: 8703.629 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#183: DNA chain DNA


Mass: 7063.597 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#184: DNA chain DNA


Mass: 9398.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#185: DNA chain DNA


Mass: 7475.869 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#186: DNA chain DNA


Mass: 5516.579 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#187: DNA chain DNA


Mass: 12855.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#188: DNA chain DNA


Mass: 9946.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#189: DNA chain DNA


Mass: 12231.930 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#190: DNA chain DNA


Mass: 14187.214 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#191: DNA chain DNA


Mass: 8325.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#192: DNA chain DNA


Mass: 9736.279 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#193: DNA chain DNA


Mass: 5475.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#194: DNA chain DNA


Mass: 9296.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#195: DNA chain DNA


Mass: 8662.617 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#196: DNA chain DNA


Mass: 9845.396 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#197: DNA chain DNA


Mass: 7219.672 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#198: DNA chain DNA


Mass: 12262.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#199: DNA chain DNA


Mass: 7132.639 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#200: DNA chain DNA


Mass: 7378.780 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#201: DNA chain DNA


Mass: 5855.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#202: DNA chain DNA


Mass: 8022.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#203: DNA chain DNA


Mass: 7368.778 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#204: DNA chain DNA


Mass: 13829.803 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#205: DNA chain DNA


Mass: 7245.725 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#206: DNA chain DNA


Mass: 17511.307 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#207: DNA chain DNA


Mass: 7433.815 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#208: DNA chain DNA


Mass: 5424.552 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#209: DNA chain DNA


Mass: 13015.353 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#210: DNA chain DNA


Mass: 7950.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#211: DNA chain DNA


Mass: 12933.347 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#212: DNA chain DNA


Mass: 7328.753 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#213: DNA chain DNA


Mass: 8117.239 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#214: DNA chain DNA


Mass: 12870.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#215: DNA chain DNA


Mass: 7045.569 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#216: DNA chain DNA


Mass: 7417.816 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#217: DNA chain DNA


Mass: 7385.766 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#218: DNA chain DNA


Mass: 5938.815 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#219: DNA chain DNA


Mass: 9838.376 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#220: DNA chain DNA


Mass: 6975.523 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#221: DNA chain DNA


Mass: 8258.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#222: DNA chain DNA


Mass: 7761.045 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#223: DNA chain DNA


Mass: 12668.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#224: DNA chain DNA


Mass: 5492.607 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#225: DNA chain DNA


Mass: 6850.496 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#226: DNA chain DNA


Mass: 10525.858 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#227: DNA chain DNA


Mass: 8919.747 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#228: DNA chain DNA


Mass: 12346.993 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#229: DNA chain DNA


Mass: 6499.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#230: DNA chain DNA


Mass: 15118.754 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#231: DNA chain DNA


Mass: 9604.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#232: DNA chain DNA


Mass: 7012.529 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#233: DNA chain DNA


Mass: 6519.261 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#234: DNA chain DNA


Mass: 5902.850 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#235: DNA chain DNA


Mass: 5516.632 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#236: DNA chain DNA


Mass: 6421.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#237: DNA chain DNA


Mass: 6960.565 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13
#238: DNA chain DNA


Mass: 18165.717 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia virus M13

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging

-
Sample preparation

ComponentName: Subvolume average of DNA signpost origami nanostructure
Type: COMPLEX / Details: DNA scaffold with DNA oligos as staples / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Escherichia virus M13
Source (recombinant)Organism: synthetic construct (others)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

-
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 defocus max: 5500 nm / Nominal defocus min: 3000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 3 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

-
Processing

SoftwareName: UCSF ChimeraX / Version: 1.1/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / Type: package
EM software
IDNameVersionCategory
1IMODvolume selection
2SerialEMimage acquisition
4IMODCTF correction
11PEETfinal Euler assignment
13PEET1.13.03D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 36.44 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 694 / Symmetry type: POINT
EM volume selectionMethod: Manual selction / Num. of tomograms: 54 / Num. of volumes extracted: 694

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