[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

TitleStructures of the mycobacterial membrane protein MmpL3 reveal its mechanism of lipid transport.
Journal, issue, pagesPLoS Biol, Vol. 19, Issue 8, Page e3001370, Year 2021
Publish dateAug 12, 2021
AuthorsChih-Chia Su / Philip A Klenotic / Meng Cui / Meinan Lyu / Christopher E Morgan / Edward W Yu /
PubMed AbstractThe mycobacterial membrane protein large 3 (MmpL3) transporter is essential and required for shuttling the lipid trehalose monomycolate (TMM), a precursor of mycolic acid (MA)-containing trehalose ...The mycobacterial membrane protein large 3 (MmpL3) transporter is essential and required for shuttling the lipid trehalose monomycolate (TMM), a precursor of mycolic acid (MA)-containing trehalose dimycolate (TDM) and mycolyl arabinogalactan peptidoglycan (mAGP), in Mycobacterium species, including Mycobacterium tuberculosis and Mycobacterium smegmatis. However, the mechanism that MmpL3 uses to facilitate the transport of fatty acids and lipidic elements to the mycobacterial cell wall remains elusive. Here, we report 7 structures of the M. smegmatis MmpL3 transporter in its unbound state and in complex with trehalose 6-decanoate (T6D) or TMM using single-particle cryo-electron microscopy (cryo-EM) and X-ray crystallography. Combined with calculated results from molecular dynamics (MD) and target MD simulations, we reveal a lipid transport mechanism that involves a coupled movement of the periplasmic domain and transmembrane helices of the MmpL3 transporter that facilitates the shuttling of lipids to the mycobacterial cell wall.
External linksPLoS Biol / PubMed:34383749 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.66 - 4.33 Å
Structure data

22724

7k8a

EMDB-22724, PDB-7k8a:
CryoEM structure of a trehalose monomycolate transporter in lipid nanodiscs
Method: EM (single particle) / Resolution: 3.65 Å

22725

7k8b

EMDB-22725, PDB-7k8b:
CryoEM structure of a trehalose monomycolate transporter in lipid nanodiscs
Method: EM (single particle) / Resolution: 2.94 Å

22726

7k8c

EMDB-22726, PDB-7k8c:
CryoEM structure of a trehalose monomycolate transporter in lipid nanodiscs
Method: EM (single particle) / Resolution: 4.27 Å

22728

7k8d

EMDB-22728, PDB-7k8d:
CryoEM structure of a trehalose monomycolate transporter in TMM lipid nanodiscs (form II)
Method: EM (single particle) / Resolution: 4.33 Å

24206

7n6b

EMDB-24206, PDB-7n6b:
Structure of MmpL3 reconstituted into lipid nanodisc in the TMM bound state
Method: EM (single particle) / Resolution: 2.66 Å

PDB-7k7m:
Crystal Structure of a membrane protein
Method: X-RAY DIFFRACTION / Resolution: 3.33 Å

Chemicals

ChemComp-0HJ:
6-O-[(2S)-2-{(1S)-18-[(1R,2R)-2-hexylcyclopropyl]-1-hydroxyoctadecyl}tricosanoyl]-alpha-D-glucopyranosyl alpha-D-glucopyranoside

Source
  • mycolicibacterium smegmatis (bacteria)
  • mycolicibacterium smegmatis (strain atcc 700084 / mc(2)155) (bacteria)
KeywordsMEMBRANE PROTEIN / transporter / TRANSLOCASE / trehalose monomycolate transporter

+
About Yorodumi Papers

-
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 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