[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 assembly of the S-layer in C. difficile.
Journal, issue, pagesNat Commun, Vol. 13, Issue 1, Page 970, Year 2022
Publish dateFeb 25, 2022
AuthorsPaola Lanzoni-Mangutchi / Oishik Banerji / Jason Wilson / Anna Barwinska-Sendra / Joseph A Kirk / Filipa Vaz / Shauna O'Beirne / Arnaud Baslé / Kamel El Omari / Armin Wagner / Neil F Fairweather / Gillian R Douce / Per A Bullough / Robert P Fagan / Paula S Salgado /
PubMed AbstractMany bacteria and archaea possess a two-dimensional protein array, or S-layer, that covers the cell surface and plays crucial roles in cell physiology. Here, we report the crystal structure of SlpA, ...Many bacteria and archaea possess a two-dimensional protein array, or S-layer, that covers the cell surface and plays crucial roles in cell physiology. Here, we report the crystal structure of SlpA, the main S-layer protein of the bacterial pathogen Clostridioides difficile, and use electron microscopy to study S-layer organisation and assembly. The SlpA crystal lattice mimics S-layer assembly in the cell, through tiling of triangular prisms above the cell wall, interlocked by distinct ridges facing the environment. Strikingly, the array is very compact, with pores of only ~10 Å in diameter, compared to other S-layers (30-100 Å). The surface-exposed flexible ridges are partially dispensable for overall structure and assembly, although a mutant lacking this region becomes susceptible to lysozyme, an important molecule in host defence. Thus, our work gives insights into S-layer organisation and provides a basis for development of C. difficile-specific therapeutics.
External linksNat Commun / PubMed:35217634 / PubMed Central
MethodsEM (electron crystallography) / X-ray diffraction
Resolution1.5 - 3.5 Å
Structure data

EMDB-13957, PDB-7qgq:
Extended H/L (SLPH/SLPL) complex from C. difficile (CD630 strain) fit into R20291 S-layer negative stain map
Method: EM (electron crystallography)

PDB-7acv:
SLPL/HID (LMW SLP complex with HMW SLP interacting domain - HID) from C. difficile (R7404 strain)
Method: X-RAY DIFFRACTION / Resolution: 2.4 Å

PDB-7acw:
LID/HID (LMW SLP and HMW SLP interacting domains) from C. difficile (R7404 strain)
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-7acx:
H/L (SLPH/SLPL) complex from C. difficile (R7404 strain)
Method: X-RAY DIFFRACTION / Resolution: 2.65 Å

PDB-7acy:
H/L (SLPH/SLPL) complex from C. difficile (CD630 strain)
Method: X-RAY DIFFRACTION / Resolution: 2.55 Å

PDB-7acz:
RdeltaD2 H/L (LMW SLP/HMW SLP) complex from C. difficile SlpA (R20291 strain)
Method: X-RAY DIFFRACTION / Resolution: 3.5 Å

Chemicals

ChemComp-HOH:
WATER / Water

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

ChemComp-SO4:
SULFATE ION / Sulfate

Source
  • clostridioides difficile r20291 (bacteria)
  • clostridioides difficile 630 (bacteria)
  • clostridioides difficile (bacteria)
  • clostridioides difficile (strain 630) (bacteria)
  • clostridioides difficile (strain r20291) (bacteria)
KeywordsSTRUCTURAL PROTEIN / bacterial surface layer protein / SLP LMW / SLP HMW interacting domain (HID) / Bacterial surface / S-layer

+
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