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Showing all 17 items for author: frydman, & j

PDB-4a0o:
Symmetry-free cryo-EM map of TRiC in the nucleotide-free (apo) state
Method: single particle / : Cong Y, Schroder GF, Meyer AS, Jakana J, Ma B, Dougherty MT, Schmid MF, Reissmann S, Levitt M, Ludtke SL, Frydman J, Chiu W

PDB-4a0v:
model refined against the Symmetry-free cryo-EM map of TRiC-AMP-PNP
Method: single particle / : Cong Y, Schroder GF, Meyer AS, Jakana J, Ma B, Dougherty MT, Schmid MF, Reissmann S, Levitt M, Ludtke SL, Frydman J, Chiu W

PDB-4a0w:
model built against symmetry-free cryo-EM map of TRiC-ADP-AlFx
Method: single particle / : Cong Y, Schroder GF, Meyer AS, Jakana J, Ma B, Dougherty MT, Schmid MF, Reissmann S, Levitt M, Ludtke SL, Frydman J, Chiu W

PDB-4a13:
model refined against symmetry-free cryo-EM map of TRiC-ADP
Method: single particle / : Cong Y, Schroder GF, Meyer AS, Jakana J, Ma B, Dougherty MT, Schmid MF, Reissmann S, Levitt M, Ludtke SL, Frydman J, Chiu W

PDB-3j02:
Lidless D386A Mm-cpn in the pre-hydrolysis ATP-bound state
Method: single particle / : Zhang J, Ma B, DiMaio F, Douglas NR, Joachimiak L, Baker D, Frydman J, Levitt M, Chiu W

PDB-3j03:
Lidless Mm-cpn in the closed state with ATP/AlFx
Method: single particle / : Zhang J, Ma B, DiMaio F, Douglas NR, Joachimiak L, Baker D, Frydman J, Levitt M, Chiu W

PDB-3izh:
Mm-cpn D386A with ATP
Method: single particle / : Douglas NR, Reissmann S, Zhang J, Chen B, Jakana J, Kumar R, Chiu W, Frydman J

PDB-3izi:
Mm-cpn rls with ATP
Method: single particle / : Douglas NR, Reissmann S, Zhang J, Chen B, Jakana J, Kumar R, Chiu W, Frydman J

PDB-3izj:
Mm-cpn rls with ATP and AlFx
Method: single particle / : Douglas NR, Reissmann S, Zhang J, Chen B, Jakana J, Kumar R, Chiu W, Frydman J

PDB-3izk:
Mm-cpn rls deltalid with ATP
Method: single particle / : Douglas NR, Reissmann S, Zhang J, Chen B, Jakana J, Kumar R, Chiu W, Frydman J

PDB-3izl:
Mm-cpn rls deltalid with ATP and AlFx
Method: single particle / : Douglas NR, Reissmann S, Zhang J, Chen B, Jakana J, Kumar R, Chiu W, Frydman J

PDB-3izm:
Mm-cpn wildtype with ATP
Method: single particle / : Douglas NR, Reissmann S, Zhang J, Chen B, Jakana J, Kumar R, Chiu W, Frydman J

PDB-3izn:
Mm-cpn deltalid with ATP
Method: single particle / : Douglas NR, Reissmann S, Zhang J, Chen B, Jakana J, Kumar R, Chiu W, Frydman J

PDB-3iyg:
Ca model of bovine TRiC/CCT derived from a 4.0 Angstrom cryo-EM map
Method: single particle / : Cong Y, Baker ML, Ludtke SJ, Frydman J, Chiu W

PDB-3ktt:
Atomic model of bovine TRiC CCT2(beta) subunit derived from a 4.0 Angstrom cryo-EM map
Method: single particle / : Cong Y, Baker ML, Ludtke SJ, Frydman J, Chiu W

PDB-3los:
Atomic Model of Mm-cpn in the Closed State
Method: single particle / : Zhang J, Baker ML, Schroeder G, Douglas NR, Reissmann S, Jakana J, Dougherty M, Fu CJ, Levitt M, Ludtke SJ, Frydman J, Chiu W

PDB-3iyf:
Atomic Model of the Lidless Mm-cpn in the Open State
Method: single particle / : Zhang J, Baker ML, Schroeder G, Douglas NR, Reissmann S, Jakana J, Dougherty M, Fu CJ, Levitt M, Ludtke SJ, Frydman J, Chiu W

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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

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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

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Jun 16, 2017. Omokage search with filter

Omokage search with filter

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Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

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Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

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Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

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  • 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

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