[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

TitleVisualizing acyl carrier protein interactions within a crosslinked type I polyketide synthase.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 7798, Year 2025
Publish dateAug 21, 2025
AuthorsZiran Jiang / Graham W Heberlig / Jeffrey A Chen / Jennifer Huynh / James J La Clair / Michael D Burkart /
PubMed AbstractUsing a combination of dual covalent crosslinking and cryo-EM analyses, we elucidate the structure of mycocerosic acid synthase from Mycobacterium tuberculosis trapped in two distinct catalytic ...Using a combination of dual covalent crosslinking and cryo-EM analyses, we elucidate the structure of mycocerosic acid synthase from Mycobacterium tuberculosis trapped in two distinct catalytic states during its iterative cycle. These structures reveal domain architecture of the acyl carrier protein mediating condensation and dehydration through dual site-selective crosslinking of the acyl carrier protein with the ketosynthase and dehydratase domains. Map density was sufficient to visualize full domain architecture with active site-bound probes and elucidate key interactions of four distinct crosslinked species. Here, iterative vectorial polyketide biosynthesis arises through an overall twisting and tilting architecture, enabling positioning and entry of the cognate substrate at each enzymatic domain. These structures present valuable details for future therapeutic design against mycocerosic acid biosynthesis in M. tuberculosis.
External linksNat Commun / PubMed:40841798 / PubMed Central
MethodsEM (single particle)
Resolution3.22 - 6.15 Å
Structure data

46504

9d2y

EMDB-46504, PDB-9d2y:
Cryo-EM structure of mycocerosic acid synthase with double KS-ACP crosslinking using C16 alpha-bromoamide. Complex A
Method: EM (single particle) / Resolution: 3.87 Å

46505

9d2z

EMDB-46505, PDB-9d2z:
Cryo-EM structure of mycocerosic acid synthase with single KS-ACP crosslink using C16 alpha-bromoamide. Complex B
Method: EM (single particle) / Resolution: 3.22 Å

46506

9d30

EMDB-46506, PDB-9d30:
Cryo-EM structure of mycocerosic acid synthase with a single DH-ACP crosslink using C16 alpha-bromoamide. Complex C
Method: EM (single particle) / Resolution: 3.74 Å

EMDB-46507: Cryo-EM structure of mycocerosic acid synthase with KS-ACP' crosslink and DH-ACP crosslink using C16 alpha-bromoamide. Complex D
Method: EM (single particle) / Resolution: 6.15 Å

Chemicals

PDB-1by8:
THE CRYSTAL STRUCTURE OF HUMAN PROCATHEPSIN K

ChemComp-MU4:
N-[2-(hexadecanoylamino)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide

Source
  • mycobacterium tuberculosis (bacteria)
KeywordsBIOSYNTHETIC PROTEIN / FAS / polyketide / crosslinked / ketosynthase / dehydratase

+
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