+Open data
Loading...
-Basic information
Entry | Database: PDB / ID: 7are | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | DNA origami pointer object v2 | ||||||||||||
Components |
| ||||||||||||
Keywords | DNA / DNA Origami | ||||||||||||
Function / homology | DNA / DNA (> 10) / DNA (> 100) / DNA (> 1000) Function and homology information | ||||||||||||
Biological species | synthetic construct (others) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.4 Å | ||||||||||||
Authors | Thomas, 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
| ||||||||||||
Citation | Journal: 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7are.cif.gz | 5.9 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7are.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7are.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ar/7are ftp://data.pdbj.org/pub/pdb/validation_reports/ar/7are | HTTPS FTP |
---|
-Related structure data
Related structure data | 11881MC 7arqC 7artC 7arvC 7aryC 7as5C M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | |
EM raw data | EMPIAR-10623 (Title: cryo-EM single particle dataset of a DNA nanostructure called "The Pointer-v2" Data size: 9.0 TB Data #1: Multi-frame micrographs of a DNA nanostructure called "The Pointer v2" [micrographs - multiframe]) |
-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
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
|
-Components
+DNA chain , 203 types, 203 molecules AAABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAXAYAZAaAbAcAd...
#1: DNA chain | Mass: 2236402.750 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
---|---|
#2: DNA chain | Mass: 12334.962 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 9506.153 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 12250.910 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#5: DNA chain | Mass: 14749.472 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#6: DNA chain | Mass: 9518.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#7: DNA chain | Mass: 12282.907 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#8: DNA chain | Mass: 9609.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#9: DNA chain | Mass: 13745.855 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#10: DNA chain | Mass: 12426.987 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#11: DNA chain | Mass: 13737.846 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#12: DNA chain | Mass: 11069.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#13: DNA chain | Mass: 13928.988 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#14: DNA chain | Mass: 12333.976 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#15: DNA chain | Mass: 12320.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#16: DNA chain | Mass: 11089.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#17: DNA chain | Mass: 13760.868 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#18: DNA chain | Mass: 10387.684 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#19: DNA chain | Mass: 11080.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#20: DNA chain | Mass: 10530.830 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#21: DNA chain | Mass: 10291.637 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#22: DNA chain | Mass: 10511.798 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#23: DNA chain | Mass: 9902.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#24: DNA chain | Mass: 13037.403 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#25: DNA chain | Mass: 12252.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#26: DNA chain | Mass: 14942.607 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#27: DNA chain | Mass: 12292.910 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#28: DNA chain | Mass: 11303.280 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#29: DNA chain | Mass: 15544.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#30: DNA chain | Mass: 12483.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#31: DNA chain | Mass: 11289.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#32: DNA chain | Mass: 14762.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#33: DNA chain | Mass: 13070.493 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#34: DNA chain | Mass: 11269.289 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#35: DNA chain | Mass: 11400.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#36: DNA chain | Mass: 9657.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#37: DNA chain | Mass: 12294.937 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#38: DNA chain | Mass: 12910.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#39: DNA chain | Mass: 12212.862 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#40: DNA chain | Mass: 12239.919 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#41: DNA chain | Mass: 9814.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#42: DNA chain | Mass: 11511.447 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#43: DNA chain | Mass: 12395.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#44: DNA chain | Mass: 12524.075 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#45: DNA chain | Mass: 9369.041 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#46: DNA chain | Mass: 9922.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#47: DNA chain | Mass: 9975.472 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#48: DNA chain | Mass: 12199.880 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#49: DNA chain | Mass: 12275.870 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#50: DNA chain | Mass: 9856.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#51: DNA chain | Mass: 12372.994 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#52: DNA chain | Mass: 12364.969 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#53: DNA chain | Mass: 14806.521 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#54: DNA chain | Mass: 9457.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#55: DNA chain | Mass: 12698.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#56: DNA chain | Mass: 9811.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#57: DNA chain | Mass: 14810.541 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#58: DNA chain | Mass: 12324.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#59: DNA chain | Mass: 12465.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#60: DNA chain | Mass: 12852.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#61: DNA chain | Mass: 11282.271 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#62: DNA chain | Mass: 12350.910 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#63: DNA chain | Mass: 9874.380 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#64: DNA chain | Mass: 13973.954 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#65: DNA chain | Mass: 11389.309 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#66: DNA chain | Mass: 9698.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#67: DNA chain | Mass: 11063.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#68: DNA chain | Mass: 12904.261 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#69: DNA chain | Mass: 11473.376 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#70: DNA chain | Mass: 12238.864 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#71: DNA chain | Mass: 9695.268 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#72: DNA chain | Mass: 12270.913 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#73: DNA chain | Mass: 9847.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#74: DNA chain | Mass: 11338.279 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#75: DNA chain | Mass: 9943.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#76: DNA chain | Mass: 9888.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#77: DNA chain | Mass: 12337.926 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#78: DNA chain | Mass: 14612.396 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#79: DNA chain | Mass: 9916.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#80: DNA chain | Mass: 12232.919 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#81: DNA chain | Mass: 14813.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#82: DNA chain | Mass: 12298.944 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#83: DNA chain | Mass: 12855.273 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#84: DNA chain | Mass: 14884.554 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#85: DNA chain | Mass: 14556.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#86: DNA chain | Mass: 12154.862 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#87: DNA chain | Mass: 12178.834 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#88: DNA chain | Mass: 12320.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#89: DNA chain | Mass: 12131.807 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#90: DNA chain | Mass: 12263.981 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#91: DNA chain | Mass: 9868.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#92: DNA chain | Mass: 12218.857 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#93: DNA chain | Mass: 12301.962 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#94: DNA chain | Mass: 13593.699 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#95: DNA chain | Mass: 9998.420 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#96: DNA chain | Mass: 12536.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#97: DNA chain | Mass: 12425.963 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#98: DNA chain | Mass: 15064.618 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#99: DNA chain | Mass: 9000.836 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#100: DNA chain | Mass: 12953.298 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#101: DNA chain | Mass: 12227.857 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#102: DNA chain | Mass: 12301.905 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#103: DNA chain | Mass: 9864.378 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#104: DNA chain | Mass: 12167.829 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#105: DNA chain | Mass: 14756.473 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#106: DNA chain | Mass: 12349.905 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#107: DNA chain | Mass: 9498.128 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#108: DNA chain | Mass: 14798.496 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#109: DNA chain | Mass: 12156.876 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#110: DNA chain | Mass: 14718.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#111: DNA chain | Mass: 12398.022 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#112: DNA chain | Mass: 12366.908 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#113: DNA chain | Mass: 12228.861 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#114: DNA chain | Mass: 12336.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#115: DNA chain | Mass: 12213.812 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#116: DNA chain | Mass: 12903.287 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#117: DNA chain | Mass: 9482.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#118: DNA chain | Mass: 12257.879 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#119: DNA chain | Mass: 14881.573 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#120: DNA chain | Mass: 15429.881 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#121: DNA chain | Mass: 9561.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#122: DNA chain | Mass: 8887.766 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#123: DNA chain | Mass: 12323.955 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#124: DNA chain | Mass: 12458.986 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#125: DNA chain | Mass: 12187.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#126: DNA chain | Mass: 10523.775 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#127: DNA chain | Mass: 12275.924 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#128: DNA chain | Mass: 12287.937 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#129: DNA chain | Mass: 10507.830 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#130: DNA chain | Mass: 9837.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#131: DNA chain | Mass: 12372.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#132: DNA chain | Mass: 12284.884 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#133: DNA chain | Mass: 12373.984 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#134: DNA chain | Mass: 12272.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#135: DNA chain | Mass: 12356.060 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#136: DNA chain | Mass: 13473.661 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#137: DNA chain | Mass: 11272.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#138: DNA chain | Mass: 12208.859 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#139: DNA chain | Mass: 12167.776 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#140: DNA chain | Mass: 14827.632 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#141: DNA chain | Mass: 10340.695 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#142: DNA chain | Mass: 12324.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#143: DNA chain | Mass: 12183.880 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#144: DNA chain | Mass: 14577.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#145: DNA chain | Mass: 14760.515 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#146: DNA chain | Mass: 10434.730 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#147: DNA chain | Mass: 8050.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#148: DNA chain | Mass: 13584.771 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#149: DNA chain | Mass: 10046.506 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#150: DNA chain | Mass: 8042.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#151: DNA chain | Mass: 12387.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#152: DNA chain | Mass: 10407.726 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#153: DNA chain | Mass: 10439.776 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#154: DNA chain | Mass: 12308.945 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#155: DNA chain | Mass: 12366.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#156: DNA chain | Mass: 12413.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#157: DNA chain | Mass: 14900.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#158: DNA chain | Mass: 14805.549 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#159: DNA chain | Mass: 14200.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#160: DNA chain | Mass: 14782.510 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#161: DNA chain | Mass: 13554.764 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#162: DNA chain | Mass: 12200.867 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#163: DNA chain | Mass: 14875.631 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#164: DNA chain | Mass: 9666.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#165: DNA chain | Mass: 13439.649 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#166: DNA chain | Mass: 9982.473 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#167: DNA chain | Mass: 12251.951 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#168: DNA chain | Mass: 15391.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#169: DNA chain | Mass: 12237.927 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#170: DNA chain | Mass: 12333.976 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#171: DNA chain | Mass: 12314.995 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#172: DNA chain | Mass: 12503.084 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#173: DNA chain | Mass: 12909.321 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#174: DNA chain | Mass: 15367.857 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#175: DNA chain | Mass: 12876.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#176: DNA chain | Mass: 12320.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#177: DNA chain | Mass: 14894.610 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#178: DNA chain | Mass: 12476.026 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#179: DNA chain | Mass: 12400.987 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#180: DNA chain | Mass: 9476.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#181: DNA chain | Mass: 12394.002 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#182: DNA chain | Mass: 12431.996 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#183: DNA chain | Mass: 13754.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#184: DNA chain | Mass: 10363.658 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#185: DNA chain | Mass: 14747.533 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#186: DNA chain | Mass: 14791.562 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#187: DNA chain | Mass: 12266.893 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#188: DNA chain | Mass: 14701.474 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#189: DNA chain | Mass: 9549.159 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#190: DNA chain | Mass: 12369.993 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#191: DNA chain | Mass: 15414.972 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#192: DNA chain | Mass: 15412.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#193: DNA chain | Mass: 12352.991 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#194: DNA chain | Mass: 12815.304 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#195: DNA chain | Mass: 11280.280 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#196: DNA chain | Mass: 14809.604 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#197: DNA chain | Mass: 12286.966 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#198: DNA chain | Mass: 9790.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#199: DNA chain | Mass: 14842.644 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#200: DNA chain | Mass: 14855.573 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#201: DNA chain | Mass: 7285.729 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#202: DNA chain | Mass: 9829.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#203: DNA chain | Mass: 12420.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: DNA origami pointer object v2 / Type: COMPLEX / Details: DNA Origami / Entity ID: all / Source: RECOMBINANT |
---|---|
Molecular weight | Experimental value: NO |
Source (natural) | Organism: synthetic construct (others) |
Source (recombinant) | Organism: synthetic construct (others) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Monodisperse, 50nM |
Specimen support | Details: Grid was coated with graphene oxide / Grid type: Quantifoil |
Vitrification | Instrument: 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 |
---|---|
Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Image recording | Electron dose: 20 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
---|---|
3D reconstruction | Resolution: 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
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of 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