[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleStructural basis of MsbA-mediated lipopolysaccharide transport.
Journal, issue, pagesNature, Vol. 549, Issue 7671, Page 233-237, Year 2017
Publish dateSep 14, 2017
AuthorsWei Mi / Yanyan Li / Sung Hwan Yoon / Robert K Ernst / Thomas Walz / Maofu Liao
External linksPubMed:28869968 / Publisher's page
MethodsEM (single particle)
Resolution4.2 - 6.9 A
Structure data

EMDB-8465:
3D cryo-EM reconstruction of MsbA-nanodisc with ADP

EMDB-8467:
Cryo-EM structure of MsbA-nanodisc with ADP-vanadate

EMDB-8469:
3D cryo-EM reconstruction of nucleotide-free MsbA in lipid nanodisc

EMDB-8669:
CryoEM map of MsbA in POPG nanodisc

EMDB-8670:
CryoEM map of MsbA with lipid A in POPG nanodisc

EMDB-8671:
CryoEM map of MsbA in POPC nanodisc

PDB-5ttp:
Cryo-EM structure of MsbA-nanodisc with ADP-vanadate

PDB-5tv4:
3D cryo-EM reconstruction of nucleotide-free MsbA in lipid nanodisc

Chemicals

ChemComp-PA1:
2-amino-2-deoxy-alpha-D-glucopyranose

ChemComp-KDO:
3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID

ChemComp-GMH:
L-GLYCERO-D-MANNO-HEPTOPYRANOSE

ChemComp-PO4:
PHOSPHATE ION

ChemComp-FTT:
3-HYDROXY-TETRADECANOIC ACID

ChemComp-MYR:
MYRISTIC ACID

ChemComp-DAO:
LAURIC ACID

SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Escherichia coli o157:h7 / bacteria / image: Escherichia coli
KeywordsHYDROLASE / ABC transporter / LPS / flippase / nanodisc

+
About Yorodumi Papers

-
News

-
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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

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

+
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)

Read more

-
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.: EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more