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- EMDB-51414: Surface-layer (S-layer) PS2 protein from Corynebacterium glutamicum -

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Basic information

Entry
Database: EMDB / ID: EMD-51414
TitleSurface-layer (S-layer) PS2 protein from Corynebacterium glutamicum
Map data
Sample
  • Organelle or cellular component: Ex vivo PS2 S-layer
    • Protein or peptide: PS2
KeywordsS-layer / Corynebacterium / Surface / STRUCTURAL PROTEIN
Function / homologymembrane / PS2
Function and homology information
Biological speciesCorynebacterium glutamicum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsSogues A / Remaut H / Sleutel M
Funding supportEuropean Union, 2 items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)ALTF-709-2021European Union
H2020 Marie Curie Actions of the European CommissionSLYDIVEuropean Union
CitationJournal: bioRxiv / Year: 2024
Title: Cryo-EM structure and polar assembly of the PS2 S-layer of .
Authors: Adrià Sogues / Mike Sleutel / Julienne Petit / Daniela Megrian / Nicolas Bayan / Anne Marie Wehenkel / Han Remaut /
Abstract: The polar-growing Corynebacteriales have a complex cell envelope architecture characterized by the presence of a specialized outer membrane composed of mycolic acids. In some Corynebacteriales, this ...The polar-growing Corynebacteriales have a complex cell envelope architecture characterized by the presence of a specialized outer membrane composed of mycolic acids. In some Corynebacteriales, this mycomembrane is further supported by a proteinaceous surface layer or 'S-layer', whose function, structure and mode of assembly remain largely enigmatic. Here, we isolated PS2 S-layers from the industrially important and determined its atomic structure by 3D cryoEM reconstruction. PS2 monomers consist of a six-helix bundle 'core', a three-helix bundle 'arm', and a C-terminal transmembrane (TM) helix. The PS2 core oligomerizes into hexameric units anchored in the mycomembrane by a channel-like coiled-coil of the TM helices. The PS2 arms mediate trimeric lattice contacts, crystallizing the hexameric units into an intricate semipermeable lattice. Using pulse-chase live cell imaging, we show that the PS2 lattice is incorporated at the poles, coincident with the actinobacterial elongasome. Finally, phylogenetic analysis shows a paraphyletic distribution and dispersed chromosomal location of PS2 in Corynebacteriales as a result of multiple recombination events and losses. These findings expand our understanding of S-layer biology and enable applications of membrane-supported self-assembling bioengineered materials.
History
DepositionAug 23, 2024-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateOct 2, 2024-
Current statusOct 2, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51414.png

Downloads & links

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Map

FileDownload / File: emd_51414.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.71 Å/pix.
x 600 pix.
= 426. Å		0.71 Å/pix.
x 600 pix.
= 426. Å		0.71 Å/pix.
x 600 pix.
= 426. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.71 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0155
Minimum - Maximum-0.05604492 - 0.109315455
Average (Standard dev.)0.000063907144 (±0.003121721)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 426.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51414_msk_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_51414_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51414_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Ex vivo PS2 S-layer

EntireName: Ex vivo PS2 S-layer
Components
  • Organelle or cellular component: Ex vivo PS2 S-layer
    • Protein or peptide: PS2

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Supramolecule #1: Ex vivo PS2 S-layer

SupramoleculeName: Ex vivo PS2 S-layer / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Corynebacterium glutamicum (bacteria)

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Macromolecule #1: PS2

MacromoleculeName: PS2 / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Corynebacterium glutamicum (bacteria)
Molecular weightTheoretical: 47.666859 KDa
Recombinant expressionOrganism: Corynebacterium glutamicum (bacteria)
SequenceString: ETNPTFNITN GFNDADGSTI QPVGPVNHTE ETLRDLTDST GAYLEEFQNG TVEEIVEAYL QVQASADGFD PSEQAAYEAF EAARVRASQ ELAASAETIT KTRESVAYAL KVDQEATAAF EAYRNALRDA AISINPDGSI NPDTSINLLI DAANAANRTD R AEIEDYAH ...String:
ETNPTFNITN GFNDADGSTI QPVGPVNHTE ETLRDLTDST GAYLEEFQNG TVEEIVEAYL QVQASADGFD PSEQAAYEAF EAARVRASQ ELAASAETIT KTRESVAYAL KVDQEATAAF EAYRNALRDA AISINPDGSI NPDTSINLLI DAANAANRTD R AEIEDYAH LYTQTDIALE TPQLAYAFQD LKALQAEVDA DFEWLGEFGI DQEDGNYVQR YHLPAVEALK AEVDARVAAI EP LRADSIA KNLEAQKSDV LVRQLFLERA TAQRDTLRVV EAIFSTSARY VELYENVENV NVENKTLRQH YSALIPNLFI AAV ANISEL NAADAEAAAY YLHWDTDLAT NDEDEAYYKA KLDFAIETYA KILFNGEVWQ EPLAYVQNLD AGARQEAADR EAAR AADEA YRAEQLRIAQ EAADAQKAIA EALAKEA

UniProtKB: PS2

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state2D array

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.4000000000000001 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 521917
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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