[English] 日本語
Yorodumi
- EMDB-52335: Corynebacterium glutamicum PS2 S-layer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52335
TitleCorynebacterium glutamicum PS2 S-layer
Map data
Sample
  • Complex: Corynebacterium glutamicum PS2 S-layer
    • Protein or peptide: PS2
KeywordsS-layer / PS2 / C. glutamicum / STRUCTURAL PROTEIN
Function / homologymembrane / PS2
Function and homology information
Biological speciesCorynebacterium glutamicum ATCC 13058 (bacteria) / Corynebacterium glutamicum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsIsbilir B / Bharat T
Funding support United Kingdom, France, European Union, 6 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_1201/31 United Kingdom
Wellcome Trust225317/Z/22/Z United Kingdom
Human Frontier Science Program (HFSP)RGY0074/2021 France
European Molecular Biology Organization (EMBO)YIP 2021European Union
Leverhulme TrustPhilip Leverhulme Prize United Kingdom
The Lister Institute of Preventive MedicineLister Prize United Kingdom
CitationJournal: PLoS Biol / Year: 2025
Title: Mapping the ultrastructural topology of the corynebacterial cell surface.
Authors: Buse Isbilir / Anna Yeates / Vikram Alva / Tanmay A M Bharat /
Abstract: Corynebacterium glutamicum is a diderm bacterium extensively used in the industrial-scale production of amino acids. Corynebacteria belong to the bacterial family Mycobacteriaceae, which is ...Corynebacterium glutamicum is a diderm bacterium extensively used in the industrial-scale production of amino acids. Corynebacteria belong to the bacterial family Mycobacteriaceae, which is characterized by a highly unusual cell envelope with an outer membrane consisting of mycolic acids, called mycomembrane. The mycomembrane is further coated by a surface (S-)layer array in C. glutamicum, making this cell envelope highly distinctive. Despite the biotechnological significance of C. glutamicum and biomedical significance of mycomembrane-containing pathogens, ultrastructural and molecular details of its distinctive cell envelope remain poorly characterized. To address this, we investigated the cell envelope of C. glutamicum using electron cryotomography and cryomicroscopy of focused ion beam-milled single and dividing cells. Our cellular imaging allowed us to map the different components of the cell envelope onto the tomographic density. Our data reveal that C. glutamicum has a variable cell envelope, with the S-layer decorating the mycomembrane in a patchy manner. We further isolated and resolved the structure of the S-layer at 3.1 Å-resolution using single particle electron cryomicroscopy. Our structure shows that the S-layer of C. glutamicum is composed of a hexagonal array of the PS2 protein, which interacts directly with the mycomembrane via an anchoring segment containing a coiled-coil motif. Bioinformatic analyses revealed that the PS2 S-layer is sparsely yet exclusively present within the Corynebacterium genus and absent in other genera of the Mycobacteriaceae family, suggesting distinct evolutionary pathways in the development of their cell envelopes. Our structural and cellular data collectively provide a topography of the unusual C. glutamicum cell surface, features of which are shared by many pathogenic and microbiome-associated bacteria, as well as by several industrially significant bacterial species.
History
DepositionDec 13, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_52335.png

Downloads & links

-
Map

FileDownload / File: emd_52335.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.22 Å/pix.
x 360 pix.
= 439.92 Å		1.22 Å/pix.
x 360 pix.
= 439.92 Å		1.22 Å/pix.
x 360 pix.
= 439.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.222 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0727
Minimum - Maximum-0.42640534 - 0.77718014
Average (Standard dev.)0.000020751488 (±0.021942036)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 439.92 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_52335_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_52335_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Corynebacterium glutamicum PS2 S-layer

EntireName: Corynebacterium glutamicum PS2 S-layer
Components
  • Complex: Corynebacterium glutamicum PS2 S-layer
    • Protein or peptide: PS2

-
Supramolecule #1: Corynebacterium glutamicum PS2 S-layer

SupramoleculeName: Corynebacterium glutamicum PS2 S-layer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Corynebacterium glutamicum ATCC 13058 (bacteria)
Molecular weightTheoretical: 53.9 KDa

-
Macromolecule #1: PS2

MacromoleculeName: PS2 / type: protein_or_peptide / ID: 1
Details: PS2 hexamer from Corynebacterium glutamicum 541 (ATCC-13058)
Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Corynebacterium glutamicum (bacteria)
Molecular weightTheoretical: 54.039098 KDa
SequenceString: MFNNRIRTAA LAGAIAISTA ASGVAIPAFA QETGTYNNTG GFNDADGSTI QPAPAVDHSE AELRDATDAT GNYLAAFQSG DIEAIVGAY IDAGVDGFDP SEEAIFKAFE AARDEATQQL AFSAETITKT RESVAYALKV DQEATEAYLA YRNALRGAAT S INPLIDAA ...String:
MFNNRIRTAA LAGAIAISTA ASGVAIPAFA QETGTYNNTG GFNDADGSTI QPAPAVDHSE AELRDATDAT GNYLAAFQSG DIEAIVGAY IDAGVDGFDP SEEAIFKAFE AARDEATQQL AFSAETITKT RESVAYALKV DQEATEAYLA YRNALRGAAT S INPLIDAA NAANRTDGSE IEIYDNIFLA SDVFTDGPLL LPAYRELVAL QTEVNEDLEW LGEFAIDNDA DNYVQRYHIP AV EALKAEI DARLEAIEPL RADSAEKNRL AQKSDVLVRQ LFLERATAQR DTLRIVEAIF ATATRYVELY ESDEDVNVEG KTL REHYFA LFPTLFGAAS FNVGVLNTAD DAVIDYYLVW DTDLETNDED AAYAEEKREF ALLTYAKIFI NGQWQEKVKY VQNL DDGAR AEAARIEAER LADEAYRAEQ LRIAQEAADA QKAIADALAK EAENNNNSGG DNSSDDKGTG SSDIGSWGPF AAIAA IIAA IAAIFPFLSG IVKF

UniProtKB: PS2

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state2D array

-
Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4SHepes
150.0 mMNaClSodium chloride
1.0 mMMgCl2Magnesium chloride
2.0 mMCaCl2Calcium chloride

Details: 50 mM HEPES pH=7.5, 150 mM NaCl, 1 mM MgCl2, 2 mM CaCl2
GridModel: Quantifoil R2/2 / Material: COPPER/RHODIUM / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV
Details: 3.5 uL of resuspended sample was applied to a freshly glow discharged Quantifoil R2/2 Cu/Rh 200 mesh grid and plunge-frozen into liquid ethane maintained at -178 C, using Vitrobot Mark IV ...Details: 3.5 uL of resuspended sample was applied to a freshly glow discharged Quantifoil R2/2 Cu/Rh 200 mesh grid and plunge-frozen into liquid ethane maintained at -178 C, using Vitrobot Mark IV after a wait time of 40 seconds, with -5 blot force and 2.5 seconds blot time..

-
Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 70.0 K / Max: 70.0 K
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.2 µm / Calibrated defocus min: 1.6 µm / Calibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.6 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

DetailsData collected with the microscope stage tilted by 30 degrees
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 50974
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
FSC plot (resolution estimation)

+
About Yorodumi

-
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

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more