[English] 日本語
Yorodumi
- PDB-7are: DNA origami pointer object v2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7are
TitleDNA origami pointer object v2
Components
  • (STAPLE STRAND) x 202
  • SCAFFOLD STRAND
KeywordsDNA / DNA Origami
Function / homologyDNA / DNA (> 10) / DNA (> 100) / DNA (> 1000)
Function and homology information
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.4 Å
AuthorsThomas, M. / Feigl, E. / Kohler, F. / Kube, M. / Nagel-Yuksel, B. / Willner, E.M. / Funke, J.J. / Gerling, T. / Stommer, P. / Honemann, M.N. ...Thomas, M. / Feigl, E. / Kohler, F. / Kube, M. / Nagel-Yuksel, B. / Willner, E.M. / Funke, J.J. / Gerling, T. / Stommer, P. / Honemann, M.N. / Martin, T.G. / Scheres, S.H.W. / Dietz, H.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
European Research Council (ERC) Germany
CitationJournal: Nat Commun / Year: 2020
Title: Revealing the structures of megadalton-scale DNA complexes with nucleotide resolution.
Authors: Massimo Kube / Fabian Kohler / Elija Feigl / Baki Nagel-Yüksel / Elena M Willner / Jonas J Funke / Thomas Gerling / Pierre Stömmer / Maximilian N Honemann / Thomas G Martin / Sjors H W ...Authors: Massimo Kube / Fabian Kohler / Elija Feigl / Baki Nagel-Yüksel / Elena M Willner / Jonas J Funke / Thomas Gerling / Pierre Stömmer / Maximilian N Honemann / Thomas G Martin / Sjors H W Scheres / Hendrik Dietz /
Abstract: The methods of DNA nanotechnology enable the rational design of custom shapes that self-assemble in solution from sets of DNA molecules. DNA origami, in which a long template DNA single strand is ...The methods of DNA nanotechnology enable the rational design of custom shapes that self-assemble in solution from sets of DNA molecules. DNA origami, in which a long template DNA single strand is folded by many short DNA oligonucleotides, can be employed to make objects comprising hundreds of unique DNA strands and thousands of base pairs, thus in principle providing many degrees of freedom for modelling complex objects of defined 3D shapes and sizes. Here, we address the problem of accurate structural validation of DNA objects in solution with cryo-EM based methodologies. By taking into account structural fluctuations, we can determine structures with improved detail compared to previous work. To interpret the experimental cryo-EM maps, we present molecular-dynamics-based methods for building pseudo-atomic models in a semi-automated fashion. Among other features, our data allows discerning details such as helical grooves, single-strand versus double-strand crossovers, backbone phosphate positions, and single-strand breaks. Obtaining this higher level of detail is a step forward that now allows designers to inspect and refine their designs with base-pair level interventions.
History
DepositionOct 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Structure summary / Category: audit_author
Revision 1.2Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-11881
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AA: SCAFFOLD STRAND
AB: STAPLE STRAND
AC: STAPLE STRAND
AD: STAPLE STRAND
AE: STAPLE STRAND
AF: STAPLE STRAND
AG: STAPLE STRAND
AH: STAPLE STRAND
AI: STAPLE STRAND
AJ: STAPLE STRAND
AK: STAPLE STRAND
AL: STAPLE STRAND
AM: STAPLE STRAND
AN: STAPLE STRAND
AO: STAPLE STRAND
AP: STAPLE STRAND
AQ: STAPLE STRAND
AR: STAPLE STRAND
AS: STAPLE STRAND
AT: STAPLE STRAND
AU: STAPLE STRAND
AV: STAPLE STRAND
AW: STAPLE STRAND
AX: STAPLE STRAND
AY: STAPLE STRAND
AZ: STAPLE STRAND
Aa: STAPLE STRAND
Ab: STAPLE STRAND
Ac: STAPLE STRAND
Ad: STAPLE STRAND
Ae: STAPLE STRAND
Af: STAPLE STRAND
Ag: STAPLE STRAND
Ah: STAPLE STRAND
Ai: STAPLE STRAND
Aj: STAPLE STRAND
Ak: STAPLE STRAND
Al: STAPLE STRAND
Am: STAPLE STRAND
An: STAPLE STRAND
Ao: STAPLE STRAND
Ap: STAPLE STRAND
Aq: STAPLE STRAND
Ar: STAPLE STRAND
As: STAPLE STRAND
At: STAPLE STRAND
Au: STAPLE STRAND
Av: STAPLE STRAND
Aw: STAPLE STRAND
Ax: STAPLE STRAND
Ay: STAPLE STRAND
Az: STAPLE STRAND
A0: STAPLE STRAND
A1: STAPLE STRAND
A2: STAPLE STRAND
A3: STAPLE STRAND
A4: STAPLE STRAND
A5: STAPLE STRAND
A6: STAPLE STRAND
A7: STAPLE STRAND
A8: STAPLE STRAND
A9: STAPLE STRAND
BA: STAPLE STRAND
BB: STAPLE STRAND
BC: STAPLE STRAND
BD: STAPLE STRAND
BE: STAPLE STRAND
BF: STAPLE STRAND
BG: STAPLE STRAND
BH: STAPLE STRAND
BI: STAPLE STRAND
BJ: STAPLE STRAND
BK: STAPLE STRAND
BL: STAPLE STRAND
BM: STAPLE STRAND
BN: STAPLE STRAND
BO: STAPLE STRAND
BP: STAPLE STRAND
BQ: STAPLE STRAND
BR: STAPLE STRAND
BS: STAPLE STRAND
BT: STAPLE STRAND
BU: STAPLE STRAND
BV: STAPLE STRAND
BW: STAPLE STRAND
BX: STAPLE STRAND
BY: STAPLE STRAND
BZ: STAPLE STRAND
Ba: STAPLE STRAND
Bb: STAPLE STRAND
Bc: STAPLE STRAND
Bd: STAPLE STRAND
Be: STAPLE STRAND
Bf: STAPLE STRAND
Bg: STAPLE STRAND
Bh: STAPLE STRAND
Bi: STAPLE STRAND
Bj: STAPLE STRAND
Bk: STAPLE STRAND
Bl: STAPLE STRAND
Bm: STAPLE STRAND
Bn: STAPLE STRAND
Bo: STAPLE STRAND
Bp: STAPLE STRAND
Bq: STAPLE STRAND
Br: STAPLE STRAND
Bs: STAPLE STRAND
Bt: STAPLE STRAND
Bu: STAPLE STRAND
Bv: STAPLE STRAND
Bw: STAPLE STRAND
Bx: STAPLE STRAND
By: STAPLE STRAND
Bz: STAPLE STRAND
B0: STAPLE STRAND
B1: STAPLE STRAND
B2: STAPLE STRAND
B3: STAPLE STRAND
B4: STAPLE STRAND
B5: STAPLE STRAND
B6: STAPLE STRAND
B7: STAPLE STRAND
B8: STAPLE STRAND
B9: STAPLE STRAND
CA: STAPLE STRAND
CB: STAPLE STRAND
CC: STAPLE STRAND
CD: STAPLE STRAND
CE: STAPLE STRAND
CF: STAPLE STRAND
CG: STAPLE STRAND
CH: STAPLE STRAND
CI: STAPLE STRAND
CJ: STAPLE STRAND
CK: STAPLE STRAND
CL: STAPLE STRAND
CM: STAPLE STRAND
CN: STAPLE STRAND
CO: STAPLE STRAND
CP: STAPLE STRAND
CQ: STAPLE STRAND
CR: STAPLE STRAND
CS: STAPLE STRAND
CT: STAPLE STRAND
CU: STAPLE STRAND
CV: STAPLE STRAND
CW: STAPLE STRAND
CX: STAPLE STRAND
CY: STAPLE STRAND
CZ: STAPLE STRAND
Ca: STAPLE STRAND
Cb: STAPLE STRAND
Cc: STAPLE STRAND
Cd: STAPLE STRAND
Ce: STAPLE STRAND
Cf: STAPLE STRAND
Cg: STAPLE STRAND
Ch: STAPLE STRAND
Ci: STAPLE STRAND
Cj: STAPLE STRAND
Ck: STAPLE STRAND
Cl: STAPLE STRAND
Cm: STAPLE STRAND
Cn: STAPLE STRAND
Co: STAPLE STRAND
Cp: STAPLE STRAND
Cq: STAPLE STRAND
Cr: STAPLE STRAND
Cs: STAPLE STRAND
Ct: STAPLE STRAND
Cu: STAPLE STRAND
Cv: STAPLE STRAND
Cw: STAPLE STRAND
Cx: STAPLE STRAND
Cy: STAPLE STRAND
Cz: STAPLE STRAND
C0: STAPLE STRAND
C1: STAPLE STRAND
C2: STAPLE STRAND
C3: STAPLE STRAND
C4: STAPLE STRAND
C5: STAPLE STRAND
C6: STAPLE STRAND
C7: STAPLE STRAND
C8: STAPLE STRAND
C9: STAPLE STRAND
DA: STAPLE STRAND
DB: STAPLE STRAND
DC: STAPLE STRAND
DD: STAPLE STRAND
DE: STAPLE STRAND
DF: STAPLE STRAND
DG: STAPLE STRAND
DH: STAPLE STRAND
DI: STAPLE STRAND
DJ: STAPLE STRAND
DK: STAPLE STRAND
DL: STAPLE STRAND
DM: STAPLE STRAND
DN: STAPLE STRAND
DO: STAPLE STRAND
DP: STAPLE STRAND
DQ: STAPLE STRAND


Theoretical massNumber of molelcules
Total (without water)4,694,699203
Polymers4,694,699203
Non-polymers00
Water0
1


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

-
Components

+
DNA chain , 203 types, 203 molecules AAABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAXAYAZAaAbAcAd...

#1: DNA chain SCAFFOLD STRAND


Mass: 2236402.750 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain STAPLE STRAND


Mass: 12334.962 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain STAPLE STRAND


Mass: 9506.153 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain STAPLE STRAND


Mass: 12250.910 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain STAPLE STRAND


Mass: 14749.472 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain STAPLE STRAND


Mass: 9518.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain STAPLE STRAND


Mass: 12282.907 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#8: DNA chain STAPLE STRAND


Mass: 9609.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#9: DNA chain STAPLE STRAND


Mass: 13745.855 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#10: DNA chain STAPLE STRAND


Mass: 12426.987 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#11: DNA chain STAPLE STRAND


Mass: 13737.846 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#12: DNA chain STAPLE STRAND


Mass: 11069.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#13: DNA chain STAPLE STRAND


Mass: 13928.988 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#14: DNA chain STAPLE STRAND


Mass: 12333.976 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#15: DNA chain STAPLE STRAND


Mass: 12320.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#16: DNA chain STAPLE STRAND


Mass: 11089.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#17: DNA chain STAPLE STRAND


Mass: 13760.868 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#18: DNA chain STAPLE STRAND


Mass: 10387.684 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#19: DNA chain STAPLE STRAND


Mass: 11080.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#20: DNA chain STAPLE STRAND


Mass: 10530.830 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#21: DNA chain STAPLE STRAND


Mass: 10291.637 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#22: DNA chain STAPLE STRAND


Mass: 10511.798 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#23: DNA chain STAPLE STRAND


Mass: 9902.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#24: DNA chain STAPLE STRAND


Mass: 13037.403 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#25: DNA chain STAPLE STRAND


Mass: 12252.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#26: DNA chain STAPLE STRAND


Mass: 14942.607 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#27: DNA chain STAPLE STRAND


Mass: 12292.910 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#28: DNA chain STAPLE STRAND


Mass: 11303.280 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#29: DNA chain STAPLE STRAND


Mass: 15544.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#30: DNA chain STAPLE STRAND


Mass: 12483.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#31: DNA chain STAPLE STRAND


Mass: 11289.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#32: DNA chain STAPLE STRAND


Mass: 14762.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#33: DNA chain STAPLE STRAND


Mass: 13070.493 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#34: DNA chain STAPLE STRAND


Mass: 11269.289 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#35: DNA chain STAPLE STRAND


Mass: 11400.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#36: DNA chain STAPLE STRAND


Mass: 9657.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#37: DNA chain STAPLE STRAND


Mass: 12294.937 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#38: DNA chain STAPLE STRAND


Mass: 12910.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#39: DNA chain STAPLE STRAND


Mass: 12212.862 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#40: DNA chain STAPLE STRAND


Mass: 12239.919 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#41: DNA chain STAPLE STRAND


Mass: 9814.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#42: DNA chain STAPLE STRAND


Mass: 11511.447 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#43: DNA chain STAPLE STRAND


Mass: 12395.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#44: DNA chain STAPLE STRAND


Mass: 12524.075 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#45: DNA chain STAPLE STRAND


Mass: 9369.041 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#46: DNA chain STAPLE STRAND


Mass: 9922.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#47: DNA chain STAPLE STRAND


Mass: 9975.472 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#48: DNA chain STAPLE STRAND


Mass: 12199.880 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#49: DNA chain STAPLE STRAND


Mass: 12275.870 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#50: DNA chain STAPLE STRAND


Mass: 9856.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#51: DNA chain STAPLE STRAND


Mass: 12372.994 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#52: DNA chain STAPLE STRAND


Mass: 12364.969 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#53: DNA chain STAPLE STRAND


Mass: 14806.521 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#54: DNA chain STAPLE STRAND


Mass: 9457.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#55: DNA chain STAPLE STRAND


Mass: 12698.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#56: DNA chain STAPLE STRAND


Mass: 9811.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#57: DNA chain STAPLE STRAND


Mass: 14810.541 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#58: DNA chain STAPLE STRAND


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


Mass: 12465.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#60: DNA chain STAPLE STRAND


Mass: 12852.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#61: DNA chain STAPLE STRAND


Mass: 11282.271 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#62: DNA chain STAPLE STRAND


Mass: 12350.910 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#63: DNA chain STAPLE STRAND


Mass: 9874.380 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#64: DNA chain STAPLE STRAND


Mass: 13973.954 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#65: DNA chain STAPLE STRAND


Mass: 11389.309 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#66: DNA chain STAPLE STRAND


Mass: 9698.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#67: DNA chain STAPLE STRAND


Mass: 11063.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#68: DNA chain STAPLE STRAND


Mass: 12904.261 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#69: DNA chain STAPLE STRAND


Mass: 11473.376 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#70: DNA chain STAPLE STRAND


Mass: 12238.864 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#71: DNA chain STAPLE STRAND


Mass: 9695.268 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#72: DNA chain STAPLE STRAND


Mass: 12270.913 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#73: DNA chain STAPLE STRAND


Mass: 9847.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#74: DNA chain STAPLE STRAND


Mass: 11338.279 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#75: DNA chain STAPLE STRAND


Mass: 9943.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#76: DNA chain STAPLE STRAND


Mass: 9888.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#77: DNA chain STAPLE STRAND


Mass: 12337.926 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#78: DNA chain STAPLE STRAND


Mass: 14612.396 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#79: DNA chain STAPLE STRAND


Mass: 9916.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#80: DNA chain STAPLE STRAND


Mass: 12232.919 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#81: DNA chain STAPLE STRAND


Mass: 14813.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#82: DNA chain STAPLE STRAND


Mass: 12298.944 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#83: DNA chain STAPLE STRAND


Mass: 12855.273 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#84: DNA chain STAPLE STRAND


Mass: 14884.554 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#85: DNA chain STAPLE STRAND


Mass: 14556.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#86: DNA chain STAPLE STRAND


Mass: 12154.862 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#87: DNA chain STAPLE STRAND


Mass: 12178.834 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#88: DNA chain STAPLE STRAND


Mass: 12320.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#89: DNA chain STAPLE STRAND


Mass: 12131.807 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#90: DNA chain STAPLE STRAND


Mass: 12263.981 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#91: DNA chain STAPLE STRAND


Mass: 9868.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#92: DNA chain STAPLE STRAND


Mass: 12218.857 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#93: DNA chain STAPLE STRAND


Mass: 12301.962 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#94: DNA chain STAPLE STRAND


Mass: 13593.699 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#95: DNA chain STAPLE STRAND


Mass: 9998.420 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#96: DNA chain STAPLE STRAND


Mass: 12536.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#97: DNA chain STAPLE STRAND


Mass: 12425.963 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#98: DNA chain STAPLE STRAND


Mass: 15064.618 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#99: DNA chain STAPLE STRAND


Mass: 9000.836 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#100: DNA chain STAPLE STRAND


Mass: 12953.298 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#101: DNA chain STAPLE STRAND


Mass: 12227.857 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#102: DNA chain STAPLE STRAND


Mass: 12301.905 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#103: DNA chain STAPLE STRAND


Mass: 9864.378 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#104: DNA chain STAPLE STRAND


Mass: 12167.829 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#105: DNA chain STAPLE STRAND


Mass: 14756.473 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#106: DNA chain STAPLE STRAND


Mass: 12349.905 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#107: DNA chain STAPLE STRAND


Mass: 9498.128 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#108: DNA chain STAPLE STRAND


Mass: 14798.496 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#109: DNA chain STAPLE STRAND


Mass: 12156.876 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#110: DNA chain STAPLE STRAND


Mass: 14718.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#111: DNA chain STAPLE STRAND


Mass: 12398.022 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#112: DNA chain STAPLE STRAND


Mass: 12366.908 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#113: DNA chain STAPLE STRAND


Mass: 12228.861 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#114: DNA chain STAPLE STRAND


Mass: 12336.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#115: DNA chain STAPLE STRAND


Mass: 12213.812 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#116: DNA chain STAPLE STRAND


Mass: 12903.287 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#117: DNA chain STAPLE STRAND


Mass: 9482.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#118: DNA chain STAPLE STRAND


Mass: 12257.879 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#119: DNA chain STAPLE STRAND


Mass: 14881.573 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#120: DNA chain STAPLE STRAND


Mass: 15429.881 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#121: DNA chain STAPLE STRAND


Mass: 9561.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#122: DNA chain STAPLE STRAND


Mass: 8887.766 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#123: DNA chain STAPLE STRAND


Mass: 12323.955 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#124: DNA chain STAPLE STRAND


Mass: 12458.986 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#125: DNA chain STAPLE STRAND


Mass: 12187.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#126: DNA chain STAPLE STRAND


Mass: 10523.775 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#127: DNA chain STAPLE STRAND


Mass: 12275.924 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#128: DNA chain STAPLE STRAND


Mass: 12287.937 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#129: DNA chain STAPLE STRAND


Mass: 10507.830 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#130: DNA chain STAPLE STRAND


Mass: 9837.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#131: DNA chain STAPLE STRAND


Mass: 12372.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#132: DNA chain STAPLE STRAND


Mass: 12284.884 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#133: DNA chain STAPLE STRAND


Mass: 12373.984 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#134: DNA chain STAPLE STRAND


Mass: 12272.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#135: DNA chain STAPLE STRAND


Mass: 12356.060 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#136: DNA chain STAPLE STRAND


Mass: 13473.661 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#137: DNA chain STAPLE STRAND


Mass: 11272.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#138: DNA chain STAPLE STRAND


Mass: 12208.859 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#139: DNA chain STAPLE STRAND


Mass: 12167.776 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#140: DNA chain STAPLE STRAND


Mass: 14827.632 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#141: DNA chain STAPLE STRAND


Mass: 10340.695 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#142: DNA chain STAPLE STRAND


Mass: 12324.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#143: DNA chain STAPLE STRAND


Mass: 12183.880 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#144: DNA chain STAPLE STRAND


Mass: 14577.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#145: DNA chain STAPLE STRAND


Mass: 14760.515 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#146: DNA chain STAPLE STRAND


Mass: 10434.730 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#147: DNA chain STAPLE STRAND


Mass: 8050.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#148: DNA chain STAPLE STRAND


Mass: 13584.771 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#149: DNA chain STAPLE STRAND


Mass: 10046.506 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#150: DNA chain STAPLE STRAND


Mass: 8042.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#151: DNA chain STAPLE STRAND


Mass: 12387.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#152: DNA chain STAPLE STRAND


Mass: 10407.726 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#153: DNA chain STAPLE STRAND


Mass: 10439.776 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#154: DNA chain STAPLE STRAND


Mass: 12308.945 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#155: DNA chain STAPLE STRAND


Mass: 12366.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#156: DNA chain STAPLE STRAND


Mass: 12413.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#157: DNA chain STAPLE STRAND


Mass: 14900.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#158: DNA chain STAPLE STRAND


Mass: 14805.549 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#159: DNA chain STAPLE STRAND


Mass: 14200.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#160: DNA chain STAPLE STRAND


Mass: 14782.510 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#161: DNA chain STAPLE STRAND


Mass: 13554.764 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#162: DNA chain STAPLE STRAND


Mass: 12200.867 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#163: DNA chain STAPLE STRAND


Mass: 14875.631 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#164: DNA chain STAPLE STRAND


Mass: 9666.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#165: DNA chain STAPLE STRAND


Mass: 13439.649 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#166: DNA chain STAPLE STRAND


Mass: 9982.473 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#167: DNA chain STAPLE STRAND


Mass: 12251.951 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#168: DNA chain STAPLE STRAND


Mass: 15391.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#169: DNA chain STAPLE STRAND


Mass: 12237.927 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#170: DNA chain STAPLE STRAND


Mass: 12333.976 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#171: DNA chain STAPLE STRAND


Mass: 12314.995 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#172: DNA chain STAPLE STRAND


Mass: 12503.084 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#173: DNA chain STAPLE STRAND


Mass: 12909.321 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#174: DNA chain STAPLE STRAND


Mass: 15367.857 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#175: DNA chain STAPLE STRAND


Mass: 12876.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#176: DNA chain STAPLE STRAND


Mass: 12320.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#177: DNA chain STAPLE STRAND


Mass: 14894.610 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#178: DNA chain STAPLE STRAND


Mass: 12476.026 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#179: DNA chain STAPLE STRAND


Mass: 12400.987 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#180: DNA chain STAPLE STRAND


Mass: 9476.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#181: DNA chain STAPLE STRAND


Mass: 12394.002 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#182: DNA chain STAPLE STRAND


Mass: 12431.996 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#183: DNA chain STAPLE STRAND


Mass: 13754.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#184: DNA chain STAPLE STRAND


Mass: 10363.658 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#185: DNA chain STAPLE STRAND


Mass: 14747.533 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#186: DNA chain STAPLE STRAND


Mass: 14791.562 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#187: DNA chain STAPLE STRAND


Mass: 12266.893 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#188: DNA chain STAPLE STRAND


Mass: 14701.474 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#189: DNA chain STAPLE STRAND


Mass: 9549.159 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#190: DNA chain STAPLE STRAND


Mass: 12369.993 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#191: DNA chain STAPLE STRAND


Mass: 15414.972 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#192: DNA chain STAPLE STRAND


Mass: 15412.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#193: DNA chain STAPLE STRAND


Mass: 12352.991 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#194: DNA chain STAPLE STRAND


Mass: 12815.304 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#195: DNA chain STAPLE STRAND


Mass: 11280.280 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#196: DNA chain STAPLE STRAND


Mass: 14809.604 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#197: DNA chain STAPLE STRAND


Mass: 12286.966 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#198: DNA chain STAPLE STRAND


Mass: 9790.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#199: DNA chain STAPLE STRAND


Mass: 14842.644 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#200: DNA chain STAPLE STRAND


Mass: 14855.573 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#201: DNA chain STAPLE STRAND


Mass: 7285.729 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#202: DNA chain STAPLE STRAND


Mass: 9829.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#203: DNA chain STAPLE STRAND


Mass: 12420.004 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 origami pointer object v2 / Type: COMPLEX / Details: DNA Origami / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: synthetic construct (others)
Source (recombinant)Organism: synthetic construct (others)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Monodisperse, 50nM
Specimen supportDetails: Grid was coated with graphene oxide / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 293 K

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 20 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 7.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 281527 / 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