[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

TitleStructure and inhibition mechanisms of Mycobacterium tuberculosis essential transporter efflux protein A.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 3139, Year 2025
Publish dateApr 1, 2025
AuthorsNitesh Kumar Khandelwal / Meghna Gupta / James E Gomez / Sulyman Barkho / Ziqiang Guan / Ashley Y Eng / Tomohiko Kawate / Sree Ganesh Balasubramani / Andrej Sali / Deborah T Hung / Robert M Stroud /
PubMed AbstractA broad chemical genetic screen in Mycobacterium tuberculosis (Mtb) identified compounds (BRD-8000.3 and BRD-9327) that inhibit the essential efflux pump EfpA. To understand the mechanisms of ...A broad chemical genetic screen in Mycobacterium tuberculosis (Mtb) identified compounds (BRD-8000.3 and BRD-9327) that inhibit the essential efflux pump EfpA. To understand the mechanisms of inhibition, we determined the structures of EfpA with these inhibitors bound at 2.7-3.4 Å resolution. Our structures reveal different mechanisms of inhibition by the two inhibitors. BRD-8000.3 binds in a tunnel contacting the lipid bilayer and extending toward the central cavity to displace the fatty acid chain of a lipid molecule bound in the apo structure, suggesting its blocking of an access route for a natural lipidic substrate. Meanwhile, BRD-9327 binds in the outer vestibule without complete blockade of the substrate path to the outside, suggesting its possible inhibition of the movement necessary for alternate access of the transporter. Our results show EfpA as a potential lipid transporter, explain the basis of the synergy of these inhibitors and their potential for combination anti-tuberculosis therapy.
External linksNat Commun / PubMed:40169593 / PubMed Central
MethodsEM (single particle)
Resolution2.7 - 3.45 Å
Structure data

44591

9bii

EMDB-44591, PDB-9bii:
Mycobacterium tuberculosis EFPA antiparallel dimer
Method: EM (single particle) / Resolution: 2.7 Å

44594

9bin

EMDB-44594, PDB-9bin:
BRD-8000.3 bound EFPA transporter of Mycobacterium tuberculosis
Method: EM (single particle) / Resolution: 3.45 Å

44598

9biq

EMDB-44598, PDB-9biq:
BRD-9327 bound EFPA transporter of Mycobacterium tuberculosis
Method: EM (single particle) / Resolution: 3.0 Å

44651

9bl7

EMDB-44651, PDB-9bl7:
Mycobacterium tuberculosis efpA parallel dimer
Method: EM (single particle) / Resolution: 3.22 Å

Chemicals

PDB-1h2v:
Structure of the human nuclear cap-binding-complex (CBC)

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

PDB-1aqr:
CU-METALLOTHIONEIN FROM SACCHAROMYCES CEREVISIAE, NMR, MINIMIZED AVERAGE STRUCTURE

PDB-1apn:
THE CRYSTALLOGRAPHIC STRUCTURE OF METAL-FREE CONCANAVALIN A AT 2.5 ANGSTROMS RESOLUTION

PDB-1atg:
AZOTOBACTER VINELANDII PERIPLASMIC MOLYBDATE-BINDING PROTEIN

Source
  • Mycobacterium tuberculosis (bacteria)
  • mycobacterium tuberculosis h37rv (bacteria)
  • Mycobacterium (bacteria)
KeywordsMEMBRANE PROTEIN / 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