[English] 日本語
EMN search
- 3DEM data search -

-
Search query


Keywords
Database
Q: What is the data source of EM Navigator?
Latest entriesEMDB:
PDB:
Q: When the data are updated?
Author
Processing method
Display mode
Sort by
Num. of entries / page
Entry
Article
Sample
Experiment
Processing
Max number of data0 for all data
File format
  • CSV format (Comma-Separated Values, for Excel, etc.)
  • TSV format (Tab Separated Values, for Excel, etc.)
  • JSON format

Yorodumi Search

-
Search result

Showing all 40 items for (Latest entries: updated map)

EMDB-0556:
Cryo-EM Map of the active Ragulator-RagA-RagC Complex
Method: single particle / : Yokom AL, Fromm SA, Hurley JH

EMDB-10291:
Structure of the Fanconi Anaemia core complex (focussed map for top region)
Method: single particle / : Shakeel S, Rajendra E, Alcon P, He S, Scheres SHW, Passmore LA

EMDB-10292:
Structure of the Fanconi Anaemia core complex (focussed map for middle region)
Method: single particle / : Shakeel S, Rajendra E, Alcon P, He S, Scheres SHW, Passmore LA

EMDB-10293:
Structure of the Fanconi Anaemia core complex (focussed map for base region)
Method: single particle / : Shakeel S, Rajendra E, Alcon P, He S, Scheres SHW, Passmore LA

EMDB-4436:
Five-fold symmetrized map of native bacteriophage P68
Method: single particle / : Hrebik D, Skubnik K, Fuzik T, Plevka P

EMDB-4437:
Asymmetric map of native bacteriophage P68
Method: single particle / : Hrebik D, Skubnik K, Fuzik T, Plevka P

EMDB-4449:
Localized reconstruction of tailknob of native bacteriophage P68
Method: single particle / : Hrebik D, Fuzik T, Skubnik K, Plevka P

EMDB-4450:
Localized reconstruction of tail-spike of bacteriophage P68
Method: single particle / : Hrebik D, Skubnik K, Fuzik T, Plevka P

EMDB-4451:
Icosahedrally averaged genome release intermediate capsid of bacteriophage P68
Method: icosahedral / : Hrebik D, Skubnik K, Fuzik T, Plevka P

EMDB-4453:
Five-fold averaged reconstruction of the genome release intermediate bacteriophage P68
Method: single particle / : Hrebik D, Skubnik K, Fuzik T, Plevka P

EMDB-4456:
Five-fold symmetric reconstruction of empty particle of bacteriophage P68
Method: single particle / : Hrebik D, Skubnik K, Fuzik T, Plevka P

EMDB-4457:
Dodecameric reconstruction of portal and tail of empty particle of bacteriophage P68 (subset without tailknob)
Method: single particle / : Hrebik D, Skubnik K, Fuzik T, Plevka P

EMDB-4458:
Dodecameric reconstruction of portal and tail of empty partice of bacteriophage P68 (subset with tailknob)
Method: single particle / : Hrebik D, Skubnik K, Fuzik T, Plevka P

EMDB-4864:
ABeta fibril morphology II
Method: helical / : Kollmer M, Fandrich M

EMDB-4866:
Abeta fibril (Morphology III)
Method: helical / : Kollmer M, Fandrich M

EMDB-4914:
E. coli DNA Gyrase - ATPase & DNA binding and cleavage domains
Method: single particle / : Vanden Broeck A, Lamour V

EMDB-4915:
E. coli DNA Gyrase - CTD & DNA binding and cleavage domain
Method: single particle / : Vanden Broeck A, Lamour V

EMDB-7884:
BG505 MD64 N332-GT5 SOSIP trimer in complex with BG18-like precursor HMP1 fragment antigen binding and base-binding RM20A3 fragment antigen binding
Method: single particle / : Torres JL, Ozorowski G, Steichen JM, Schief WR, Ward AB

EMDB-7885:
BG505 MD64 N332-GT5 SOSIP trimer in complex with BG18-like precursor HMP42 fragment antigen binding and base-binding RM20A3 fragment antigen binding
Method: single particle / : Torres JL, Ozorowski G, Steichen JM, Schief WR, Ward AB

EMDB-10131:
MKLP2-decocrated 13 protofilament microtubule (ADP.Al.Fx state) processed with MiRP (Microtubule Relion-based Pipeline)
Method: single particle / : Cook AC, Manka SW, Wang S, Moores CA, Atherton J

EMDB-10195:
Doublecortin N-terminal DC-domain (NDC)-decorated 13-protofilament microtubule (GDP state) processed with MiRP (Microtubule Relion-based Pipeline)
Method: helical / : Cook AC, Manka SW, Wang S, Moores CA, Atherton J

EMDB-20099:
Prohead 2 of the phage T5
Method: icosahedral / : Huet A, Duda RL, Boulanger P, Conway JF

EMDB-9931:
Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E1 state class1)
Method: single particle / : Hiraizumi M, Yamashita K, Nishizawa T, Nureki O

EMDB-9932:
Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E1 state class2)
Method: single particle / : Hiraizumi M, Yamashita K, Nishizawa T, Nureki O

EMDB-9933:
Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E1 state class3)
Method: single particle / : Hiraizumi M, Yamashita K, Nishizawa T, Nureki O

EMDB-9934:
Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E1-ATP state class2)
Method: single particle / : Hiraizumi M, Yamashita K, Nishizawa T, Nureki O

EMDB-9935:
Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E1-ATP state class1)
Method: single particle / : Hiraizumi M, Yamashita K, Nishizawa T, Nureki O

EMDB-9936:
Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E1-ATP state class3)
Method: single particle / : Hiraizumi M, Yamashita K, Nishizawa T, Nureki O

EMDB-9937:
Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E1-ADP-Pi state)
Method: single particle / : Hiraizumi M, Yamashita K, Nishizawa T, Nureki O

EMDB-9938:
Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E2P state class1)
Method: single particle / : Hiraizumi M, Yamashita K, Nishizawa T, Nureki O

EMDB-9939:
Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E2P state class2)
Method: single particle / : Hiraizumi M, Yamashita K, Nishizawa T, Nureki O

EMDB-9940:
Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E2P state class3)
Method: single particle / : Hiraizumi M, Yamashita K, Nishizawa T, Nureki O

EMDB-9941:
Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E2Pi-PL state)
Method: single particle / : Hiraizumi M, Yamashita K, Nishizawa T, Nureki O

EMDB-9942:
Cryo-EM structure of the human P4-type flippase ATP8A1-CDC50 (E1P state)
Method: single particle / : Hiraizumi M, Yamashita K, Nishizawa T, Nureki O

EMDB-9136:
Cryo-EM of self-assembly peptide filament HEAT_R1
Method: helical / : Wang F, Hughes SA, Orlova A, Conticello VP, Egelman EH

EMDB-0565:
Extracellular factors prime enterovirus particles for uncoating
Method: icosahedral / : Domanska A, Ruokolainen V, Pelliccia M, Laajala M, Butcher SJ, Marjomaki VS

EMDB-0522:
Ebola virus nucleoprotein - RNA complex
Method: helical / : Kirchdoerfer RN, Ward AB

EMDB-9031:
Cryo-EM structure of Woodchuck hepatitis virus capsid
Method: icosahedral / : Zhao Z, Wang JC, Zlotnick A

EMDB-4698:
Mouse apoferritin from data collected at liquid helium temperature
Method: single particle / : Pfeil-Gardiner O, Mills DJ, Vonck J, Kuehlbrandt W

EMDB-4698:
Mouse apoferritin from data collected at liquid helium temperature
Method: single particle / : Pfeil-Gardiner O, Mills DJ, Vonck J, Kuehlbrandt W

+
About EMN search

-
News

-
Jul 5, 2019. Downlodablable text data

Downlodablable text data

  • Some data of EM Navigator services can be downloaded as text file. Software such as Excel can load the data files.
    PageDataFormat
    EMN Searchsearch resultCSV, TSV, or JSON
    EMN statisticsdata tableCSV or TSV

Related info.: EMN Search / EMN Statistics

-
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. (see PDBe EMDB page)
  • 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 at PDBe / Contact to PDBj

+
Feb 20, 2018. PDBj/BINDS workshop in Osaka University

PDBj/BINDS workshop in Osaka University

    +
    Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

    Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

    • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
    • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
    • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

    External links: The 2017 Nobel Prize in Chemistry - Press Release

    +
    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. See below links for details.
    • 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

    Read more

    -
    EMN Search

    3DEM data search

    • Advanced data search for EMDB and EM data in PDB widh various search and display options

    Related info.: EMDB / PDB / EM Navigator / Q: What is the data source of EM Navigator? / Yorodumi Search / Jul 5, 2019. Downlodablable text data

    Read more