[English] 日本語
Yorodumi
- PDB-6by7: Folding DNA into a lipid-conjugated nano-barrel for controlled re... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6by7
TitleFolding DNA into a lipid-conjugated nano-barrel for controlled reconstitution of membrane proteins
Components
  • (DNA (26-MER)) x 5
  • (DNA (32-MER)) x 19
  • (DNA (37-MER)) x 5
  • (DNA (38-MER)) x 2
  • (DNA (40-MER)) x 20
  • (DNA (46-MER)) x 3
  • (DNA (47-MER)) x 3
  • (DNA (48-MER)) x 27
  • (DNA (52-MER)) x 3
  • (DNA (55-MER)) x 3
  • (DNA (56-MER)) x 6
  • (DNA (58-MER)) x 2
  • DNA (27-MER)
  • DNA (29-MER)
  • DNA (35-MER)
  • DNA (36-MER)
  • DNA (4346-MER)
  • DNA (5'-D(*AP*AP*TP*AP*AP*CP*GP*GP*CP*TP*CP*AP*GP*AP*GP*C)-3')
  • DNA (5'-D(*CP*GP*AP*CP*AP*GP*AP*AP*TP*GP*AP*AP*AP*GP*AP*G)-3')
  • DNA (5'-D(*CP*GP*CP*CP*AP*CP*CP*AP*GP*AP*TP*TP*CP*AP*TP*C)-3')
  • DNA (5'-D(*GP*TP*GP*CP*CP*TP*AP*AP*GP*GP*AP*TP*AP*TP*TP*C)-3')
  • DNA (5'-D(*TP*AP*TP*TP*AP*GP*CP*GP*AP*GP*AP*TP*GP*GP*TP*TP*TP*TP*AP*TP*TP*AP*CP*A)-3')
  • DNA (5'-D(*TP*CP*AP*AP*CP*CP*GP*AP*GP*CP*TP*TP*GP*CP*TP*T)-3')
  • DNA (5'-D(P*CP*AP*TP*AP*AP*CP*GP*CP*AP*TP*AP*AP*AP*AP*CP*GP*AP*GP*GP*AP*GP*GP*TP*T)-3')
  • DNA (5'-D(P*CP*CP*AP*GP*TP*GP*CP*CP*AP*AP*AP*TP*CP*CP*GP*C)-3')
  • DNA (5'-D(P*CP*CP*CP*CP*CP*AP*GP*CP*TP*GP*GP*TP*CP*AP*TP*A)-3')
  • DNA (5'-D(P*CP*TP*GP*GP*CP*CP*TP*TP*CP*CP*TP*GP*TP*AP*GP*CP*CP*AP*AP*AP*AP*AP*TP*A)-3')
  • DNA (5'-D(P*GP*AP*CP*AP*GP*AP*TP*GP*CP*GP*TP*GP*CP*CP*AP*G)-3')
  • DNA (5'-D(P*TP*CP*GP*AP*GP*GP*TP*GP*AP*TP*TP*CP*GP*CP*GP*T)-3')
  • DNA (5'-D(P*TP*TP*TP*GP*TP*TP*AP*AP*AP*AP*CP*CP*GP*AP*TP*A)-3')
  • DNA (51-MER)
  • DNA (59-MER)
KeywordsDNA / DNA nano-barrel DNA origami DNA assembly
Function / homologyDNA / DNA (> 10) / DNA (> 100) / DNA (> 1000)
Function and homology information
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.5 Å
AuthorsDong, Y. / Chen, S. / Zhang, S. / Sodroski, J. / Yang, Z. / Liu, D. / Mao, Y.
Funding support China, United States, 7items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)11774012 China
National Natural Science Foundation of China (NSFC)91530321 China
National Natural Science Foundation of China (NSFC) China
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI93256 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI24982 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI100645 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI24755 United States
CitationJournal: Angew Chem Int Ed Engl / Year: 2018
Title: Folding DNA into a Lipid-Conjugated Nanobarrel for Controlled Reconstitution of Membrane Proteins.
Authors: Yuanchen Dong / Shuobing Chen / Shijian Zhang / Joseph Sodroski / Zhongqiang Yang / Dongsheng Liu / Youdong Mao /
Abstract: Building upon DNA origami technology, we introduce a method to reconstitute a single membrane protein into a self-assembled DNA nanobarrel that scaffolds a nanodisc-like lipid environment. Compared ...Building upon DNA origami technology, we introduce a method to reconstitute a single membrane protein into a self-assembled DNA nanobarrel that scaffolds a nanodisc-like lipid environment. Compared with the membrane-scaffolding-protein nanodisc technique, our approach gives rise to defined stoichiometry, controlled sizes, as well as enhanced stability and homogeneity in membrane protein reconstitution. We further demonstrate potential applications of the DNA nanobarrels in the structural analysis of membrane proteins.
History
DepositionDec 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-7304
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1A: DNA (52-MER)
1B: DNA (55-MER)
1C: DNA (5'-D(*AP*AP*TP*AP*AP*CP*GP*GP*CP*TP*CP*AP*GP*AP*GP*C)-3')
1D: DNA (59-MER)
1E: DNA (51-MER)
1F: DNA (46-MER)
1G: DNA (5'-D(*TP*CP*AP*AP*CP*CP*GP*AP*GP*CP*TP*TP*GP*CP*TP*T)-3')
1H: DNA (48-MER)
1I: DNA (47-MER)
1J: DNA (5'-D(*TP*AP*TP*TP*AP*GP*CP*GP*AP*GP*AP*TP*GP*GP*TP*TP*TP*TP*AP*TP*TP*AP*CP*A)-3')
1K: DNA (46-MER)
1L: DNA (5'-D(*CP*GP*AP*CP*AP*GP*AP*AP*TP*GP*AP*AP*AP*GP*AP*G)-3')
1M: DNA (32-MER)
1O: DNA (40-MER)
1P: DNA (46-MER)
1Q: DNA (37-MER)
1R: DNA (48-MER)
1S: DNA (37-MER)
1T: DNA (5'-D(*CP*GP*CP*CP*AP*CP*CP*AP*GP*AP*TP*TP*CP*AP*TP*C)-3')
1U: DNA (40-MER)
1V: DNA (26-MER)
1W: DNA (40-MER)
1X: DNA (48-MER)
1Y: DNA (27-MER)
1Z: DNA (26-MER)
1a: DNA (47-MER)
1b: DNA (32-MER)
1c: DNA (40-MER)
1d: DNA (40-MER)
1e: DNA (26-MER)
1f: DNA (40-MER)
1g: DNA (48-MER)
1h: DNA (48-MER)
1i: DNA (48-MER)
1j: DNA (32-MER)
1k: DNA (40-MER)
1l: DNA (48-MER)
1m: DNA (5'-D(P*TP*CP*GP*AP*GP*GP*TP*GP*AP*TP*TP*CP*GP*CP*GP*T)-3')
1n: DNA (56-MER)
1o: DNA (40-MER)
1p: DNA (40-MER)
1q: DNA (48-MER)
1r: DNA (32-MER)
1s: DNA (32-MER)
1t: DNA (32-MER)
1u: DNA (48-MER)
1v: DNA (5'-D(P*CP*CP*CP*CP*CP*AP*GP*CP*TP*GP*GP*TP*CP*AP*TP*A)-3')
1w: DNA (40-MER)
1x: DNA (5'-D(P*GP*AP*CP*AP*GP*AP*TP*GP*CP*GP*TP*GP*CP*CP*AP*G)-3')
2N: DNA (48-MER)
2A: DNA (40-MER)
2B: DNA (48-MER)
2C: DNA (40-MER)
2D: DNA (29-MER)
2E: DNA (5'-D(P*CP*AP*TP*AP*AP*CP*GP*CP*AP*TP*AP*AP*AP*AP*CP*GP*AP*GP*GP*AP*GP*GP*TP*T)-3')
2F: DNA (32-MER)
2G: DNA (26-MER)
2H: DNA (40-MER)
2I: DNA (40-MER)
2J: DNA (58-MER)
2K: DNA (52-MER)
2L: DNA (40-MER)
2M: DNA (48-MER)
2O: DNA (48-MER)
2P: DNA (32-MER)
2Q: DNA (58-MER)
2R: DNA (56-MER)
2S: DNA (52-MER)
2T: DNA (37-MER)
2U: DNA (48-MER)
2V: DNA (48-MER)
2W: DNA (32-MER)
2X: DNA (32-MER)
2Y: DNA (48-MER)
2Z: DNA (48-MER)
2a: DNA (5'-D(P*TP*TP*TP*GP*TP*TP*AP*AP*AP*AP*CP*CP*GP*AP*TP*A)-3')
2b: DNA (32-MER)
2c: DNA (32-MER)
2d: DNA (40-MER)
2e: DNA (5'-D(P*CP*TP*GP*GP*CP*CP*TP*TP*CP*CP*TP*GP*TP*AP*GP*CP*CP*AP*AP*AP*AP*AP*TP*A)-3')
2f: DNA (32-MER)
2g: DNA (40-MER)
2h: DNA (32-MER)
2i: DNA (32-MER)
2j: DNA (47-MER)
2k: DNA (5'-D(P*CP*CP*AP*GP*TP*GP*CP*CP*AP*AP*AP*TP*CP*CP*GP*C)-3')
2l: DNA (40-MER)
2m: DNA (48-MER)
2n: DNA (48-MER)
2o: DNA (48-MER)
2p: DNA (56-MER)
2q: DNA (56-MER)
2r: DNA (32-MER)
2s: DNA (48-MER)
2t: DNA (37-MER)
2u: DNA (55-MER)
2v: DNA (48-MER)
2w: DNA (38-MER)
2x: DNA (32-MER)
3N: DNA (4346-MER)
3A: DNA (40-MER)
3B: DNA (40-MER)
3C: DNA (48-MER)
3D: DNA (48-MER)
3E: DNA (48-MER)
3F: DNA (56-MER)
3G: DNA (5'-D(*GP*TP*GP*CP*CP*TP*AP*AP*GP*GP*AP*TP*AP*TP*TP*C)-3')
3H: DNA (56-MER)
3I: DNA (36-MER)
3J: DNA (35-MER)
3S: DNA (32-MER)
3K: DNA (48-MER)
3L: DNA (37-MER)
3M: DNA (55-MER)
3O: DNA (48-MER)
3P: DNA (38-MER)
3Q: DNA (26-MER)
3R: DNA (32-MER)


Theoretical massNumber of molelcules
Total (without water)2,715,216118
Polymers2,715,216118
Non-polymers00
Water0
1


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

-
Components

+
DNA chain , 118 types, 118 molecules 1A1B1C1D1E1F1G1H1I1J1K1L1M1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e...

#1: DNA chain DNA (52-MER)


Mass: 16252.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (55-MER)


Mass: 17104.982 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*AP*TP*AP*AP*CP*GP*GP*CP*TP*CP*AP*GP*AP*GP*C)-3')


Mass: 4916.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (59-MER)


Mass: 18351.828 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain DNA (51-MER)


Mass: 15813.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (46-MER)


Mass: 14285.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain DNA (5'-D(*TP*CP*AP*AP*CP*CP*GP*AP*GP*CP*TP*TP*GP*CP*TP*T)-3')


Mass: 4849.153 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#8: DNA chain DNA (48-MER)


Mass: 14657.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#9: DNA chain DNA (47-MER)


Mass: 14615.378 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#10: DNA chain DNA (5'-D(*TP*AP*TP*TP*AP*GP*CP*GP*AP*GP*AP*TP*GP*GP*TP*TP*TP*TP*AP*TP*TP*AP*CP*A)-3')


Mass: 7413.811 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#11: DNA chain DNA (46-MER)


Mass: 14231.138 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#12: DNA chain DNA (5'-D(*CP*GP*AP*CP*AP*GP*AP*AP*TP*GP*AP*AP*AP*GP*AP*G)-3')


Mass: 4989.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#13: DNA chain DNA (32-MER)


Mass: 9733.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#14: DNA chain DNA (40-MER)


Mass: 12172.875 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#15: DNA chain DNA (46-MER)


Mass: 14264.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#16: DNA chain DNA (37-MER)


Mass: 11315.330 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#17: DNA chain DNA (48-MER)


Mass: 14715.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#18: DNA chain DNA (37-MER)


Mass: 11477.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#19: DNA chain DNA (5'-D(*CP*GP*CP*CP*AP*CP*CP*AP*GP*AP*TP*TP*CP*AP*TP*C)-3')


Mass: 4803.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#20: DNA chain DNA (40-MER)


Mass: 12405.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#21: DNA chain DNA (26-MER)


Mass: 7880.075 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#22: DNA chain DNA (40-MER)


Mass: 12479.059 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#23: DNA chain DNA (48-MER)


Mass: 14788.543 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#24: DNA chain DNA (27-MER)


Mass: 8218.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#25: DNA chain DNA (26-MER)


Mass: 7996.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#26: DNA chain DNA (47-MER)


Mass: 14509.433 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#27: DNA chain DNA (32-MER)


Mass: 9986.479 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#28: DNA chain DNA (40-MER)


Mass: 12342.001 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#29: DNA chain DNA (40-MER)


Mass: 12409.065 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#30: DNA chain DNA (26-MER)


Mass: 7900.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#31: DNA chain DNA (40-MER)


Mass: 12135.831 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#32: DNA chain DNA (48-MER)


Mass: 14771.557 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#33: DNA chain DNA (48-MER)


Mass: 14928.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#34: DNA chain DNA (48-MER)


Mass: 14838.587 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#35: DNA chain DNA (32-MER)


Mass: 9907.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#36: DNA chain DNA (40-MER)


Mass: 12445.030 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#37: DNA chain DNA (48-MER)


Mass: 14773.496 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#38: DNA chain DNA (5'-D(P*TP*CP*GP*AP*GP*GP*TP*GP*AP*TP*TP*CP*GP*CP*GP*T)-3')


Mass: 4945.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#39: DNA chain DNA (56-MER)


Mass: 17281.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#40: DNA chain DNA (40-MER)


Mass: 12362.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#41: DNA chain DNA (40-MER)


Mass: 12283.932 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#42: DNA chain DNA (48-MER)


Mass: 14777.501 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#43: DNA chain DNA (32-MER)


Mass: 9852.330 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#44: DNA chain DNA (32-MER)


Mass: 9784.329 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#45: DNA chain DNA (32-MER)


Mass: 9818.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#46: DNA chain DNA (48-MER)


Mass: 14806.482 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#47: DNA chain DNA (5'-D(P*CP*CP*CP*CP*CP*AP*GP*CP*TP*GP*GP*TP*CP*AP*TP*A)-3')


Mass: 4819.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#48: DNA chain DNA (40-MER)


Mass: 12192.841 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#49: DNA chain DNA (5'-D(P*GP*AP*CP*AP*GP*AP*TP*GP*CP*GP*TP*GP*CP*CP*AP*G)-3')


Mass: 4948.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#50: DNA chain DNA (48-MER)


Mass: 11091.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#51: DNA chain DNA (40-MER)


Mass: 9988.455 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#52: DNA chain DNA (48-MER)


Mass: 14684.471 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#53: DNA chain DNA (40-MER)


Mass: 7965.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#54: DNA chain DNA (29-MER)


Mass: 9809.396 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#55: DNA chain DNA (5'-D(P*CP*AP*TP*AP*AP*CP*GP*CP*AP*TP*AP*AP*AP*AP*CP*GP*AP*GP*GP*AP*GP*GP*TP*T)-3')


Mass: 12293.951 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#56: DNA chain DNA (32-MER)


Mass: 14877.569 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#57: DNA chain DNA (26-MER)


Mass: 12357.945 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#58: DNA chain DNA (40-MER)


Mass: 12160.897 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#59: DNA chain DNA (40-MER)


Mass: 4937.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#60: DNA chain DNA (58-MER)


Mass: 9007.821 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#61: DNA chain DNA (52-MER)


Mass: 7435.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#62: DNA chain DNA (40-MER)


Mass: 9832.380 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#63: DNA chain DNA (48-MER)


Mass: 7347.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#64: DNA chain DNA (48-MER)


Mass: 8009.214 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#65: DNA chain DNA (32-MER)


Mass: 12364.969 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#66: DNA chain DNA (58-MER)


Mass: 12319.951 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#67: DNA chain DNA (56-MER)


Mass: 12368.003 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#68: DNA chain DNA (52-MER)


Mass: 17934.527 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#69: DNA chain DNA (37-MER)


Mass: 7433.815 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#70: DNA chain DNA (48-MER)


Mass: 15962.277 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#71: DNA chain DNA (48-MER)


Mass: 12291.920 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#72: DNA chain DNA (32-MER)


Mass: 14855.573 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#73: DNA chain DNA (32-MER)


Mass: 14691.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#74: DNA chain DNA (48-MER)


Mass: 9875.366 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#75: DNA chain DNA (48-MER)


Mass: 12324.960 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#76: DNA chain DNA (5'-D(P*TP*TP*TP*GP*TP*TP*AP*AP*AP*AP*CP*CP*GP*AP*TP*A)-3')


Mass: 17768.449 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#77: DNA chain DNA (32-MER)


Mass: 17303.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#78: DNA chain DNA (32-MER)


Mass: 13770.925 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#79: DNA chain DNA (40-MER)


Mass: 16155.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#80: DNA chain DNA (5'-D(P*CP*TP*GP*GP*CP*CP*TP*TP*CP*CP*TP*GP*TP*AP*GP*CP*CP*AP*AP*AP*AP*AP*TP*A)-3')


Mass: 11523.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#81: DNA chain DNA (32-MER)


Mass: 14698.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#82: DNA chain DNA (40-MER)


Mass: 14644.451 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#83: DNA chain DNA (32-MER)


Mass: 17385.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#84: DNA chain DNA (32-MER)


Mass: 9924.458 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#85: DNA chain DNA (47-MER)


Mass: 4913.203 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#86: DNA chain DNA (5'-D(P*CP*CP*AP*GP*TP*GP*CP*CP*AP*AP*AP*TP*CP*CP*GP*C)-3')


Mass: 9818.357 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#87: DNA chain DNA (40-MER)


Mass: 14749.506 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#88: DNA chain DNA (48-MER)


Mass: 14807.575 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#89: DNA chain DNA (48-MER)


Mass: 4896.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#90: DNA chain DNA (48-MER)


Mass: 9853.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#91: DNA chain DNA (56-MER)


Mass: 9889.339 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#92: DNA chain DNA (56-MER)


Mass: 12166.788 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#93: DNA chain DNA (32-MER)


Mass: 7313.744 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#94: DNA chain DNA (48-MER)


Mass: 9853.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#95: DNA chain DNA (37-MER)


Mass: 12388.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#96: DNA chain DNA (55-MER)


Mass: 9826.329 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#97: DNA chain DNA (48-MER)


Mass: 9836.295 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#98: DNA chain DNA (38-MER)


Mass: 14612.500 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#99: DNA chain DNA (32-MER)


Mass: 4828.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#100: DNA chain DNA (4346-MER)


Mass: 1340942.500 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#101: DNA chain DNA (40-MER)


Mass: 12622.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#102: DNA chain DNA (40-MER)


Mass: 12315.930 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#103: DNA chain DNA (48-MER)


Mass: 14785.527 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#104: DNA chain DNA (48-MER)


Mass: 15025.617 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#105: DNA chain DNA (48-MER)


Mass: 14902.565 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#106: DNA chain DNA (56-MER)


Mass: 17068.980 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#107: DNA chain DNA (5'-D(*GP*TP*GP*CP*CP*TP*AP*AP*GP*GP*AP*TP*AP*TP*TP*C)-3')


Mass: 4913.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#108: DNA chain DNA (56-MER)


Mass: 17208.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#109: DNA chain DNA (36-MER)


Mass: 11087.128 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#110: DNA chain DNA (35-MER)


Mass: 10756.936 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#111: DNA chain DNA (32-MER)


Mass: 9864.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#112: DNA chain DNA (48-MER)


Mass: 14853.579 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#113: DNA chain DNA (37-MER)


Mass: 11450.310 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#114: DNA chain DNA (55-MER)


Mass: 16991.945 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#115: DNA chain DNA (48-MER)


Mass: 14817.581 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#116: DNA chain DNA (38-MER)


Mass: 11806.624 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#117: DNA chain DNA (26-MER)


Mass: 8088.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#118: DNA chain DNA (32-MER)


Mass: 10016.448 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: DNA nano-barrel / Type: COMPLEX / Entity ID: #1-#100 / Source: MULTIPLE SOURCES
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: synthetic construct (others)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 23500 X / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 180 K / Temperature (min): 180 K
Image recordingElectron dose: 48 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 30

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 108931 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more