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- PDB-9gk2: Surface-layer (S-layer) PS2 protein from Corynebacterium glutamicum -

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Basic information

Entry
Database: PDB / ID: 9gk2
TitleSurface-layer (S-layer) PS2 protein from Corynebacterium glutamicum
ComponentsPS2
KeywordsSTRUCTURAL PROTEIN / S-layer / Corynebacterium / Surface
Function / homologymembrane / PS2
Function and homology information
Biological speciesCorynebacterium glutamicum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsSogues, A. / Remaut, H. / Sleutel, M.
Funding supportEuropean Union, 2items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: PS2
H: PS2
I: PS2
J: PS2
K: PS2
L: PS2
M: PS2
N: PS2
O: PS2
P: PS2
Q: PS2
R: PS2
S: PS2
T: PS2
U: PS2
V: PS2
W: PS2
X: PS2


Theoretical massNumber of molelcules
Total (without water)858,00318
Polymers858,00318
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
PS2


Mass: 47666.859 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: csp2 / Production host: Corynebacterium glutamicum (bacteria) / References: UniProt: Q04985

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ex vivo PS2 S-layer / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL
Source (natural)Organism: Corynebacterium glutamicum (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 60.3 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21_5207: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 521917 / Symmetry type: POINT

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