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- EMDB-50640: Corynebacterium glutamicum PS2 S-layer -

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Basic information

Entry
Database: EMDB / ID: EMD-50640
TitleCorynebacterium glutamicum PS2 S-layer
Map data
Sample
  • Organelle or cellular component: Structure of Hexagonally Packed PS2 Protein
    • Protein or peptide: PS2 - Corynebacterium glutamicum S-layer protein
KeywordsS-layer protein / 2D-lattice / hexagonal lattice / STRUCTURAL PROTEIN
Function / homologymembrane / PS2
Function and homology information
Biological speciesCorynebacterium glutamicum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 16.87 Å
AuthorsIsbilir B / Bharat TAM
Funding support United Kingdom, France, European Union, 6 items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)MRC MC_UP_1201/31 United Kingdom
Human Frontier Science Program (HFSP)RGY0074/2021 France
Wellcome Trust225317/Z/22/Z United Kingdom
European Molecular Biology Organization (EMBO)YIPEuropean Union
Leverhulme TrustPhilip Leverhulme Prize United Kingdom
The Lister Institute of Preventive MedicineLister Prize United Kingdom
CitationJournal: Biorxiv / Year: 2024
Title: Punctuated and continuous structural diversity of S-layers across the prokaryotic tree of life
Authors: Johnston E / Isbilir B / Alva V / Bharat TAM / Doye JPK
History
DepositionJun 14, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50640.png

Downloads & links

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Map

FileDownload / File: emd_50640.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.3 Å/pix.
x 150 pix.
= 494.4 Å		3.3 Å/pix.
x 150 pix.
= 494.4 Å		3.3 Å/pix.
x 150 pix.
= 494.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.296 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0934
Minimum - Maximum-0.2717295 - 0.6483061
Average (Standard dev.)0.0015018218 (±0.03477807)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 494.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map

Fileemd_50640_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_50640_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_50640_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of Hexagonally Packed PS2 Protein

EntireName: Structure of Hexagonally Packed PS2 Protein
Components
  • Organelle or cellular component: Structure of Hexagonally Packed PS2 Protein
    • Protein or peptide: PS2 - Corynebacterium glutamicum S-layer protein

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Supramolecule #1: Structure of Hexagonally Packed PS2 Protein

SupramoleculeName: Structure of Hexagonally Packed PS2 Protein / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Corynebacterium glutamicum (bacteria) / Strain: ATCC13058 / Location in cell: extracellular
Molecular weightTheoretical: 54 KDa

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Macromolecule #1: PS2 - Corynebacterium glutamicum S-layer protein

MacromoleculeName: PS2 - Corynebacterium glutamicum S-layer protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Corynebacterium glutamicum (bacteria)
SequenceString: MFNNRIRTAA LAGAIAISTA ASGVAIPAFA QETGTYNNTG GFNDADGSTI QPAPAVDHSE AELRDATDA TGNYLAAFQS GDIEAIVGAY IDVGVDGFDP SEEAIFKAFE AARDEATQQL A FSAETITK TRESVAYALK VDQEATEAYL AYRNALRGAA TSINPLIDAA ...String:
MFNNRIRTAA LAGAIAISTA ASGVAIPAFA QETGTYNNTG GFNDADGSTI QPAPAVDHSE AELRDATDA TGNYLAAFQS GDIEAIVGAY IDVGVDGFDP SEEAIFKAFE AARDEATQQL A FSAETITK TRESVAYALK VDQEATEAYL AYRNALRGAA TSINPLIDAA NAANRTDGSE IE IYDNIFL ASDVFTDGPL LLPAYRELVA LQTEVNEDLE WLGEFAIDND ADNYVQRYHI PAV EALKAE IDARLEAIEP HRADSAEKNR LAQKSDVLVR QLFLERATAQ RDTLRIVEAI FATA TRYVE LYESDENINV ENKTLREHYF ALFPTLFGAA SFNVGVLNTA DDAAIDYYLV WDTDL ETND EDAAYAEEKR EFALLTYAKI FINGQWQEKV KYVQNLDDGA RAEAARIEAE RLADEA YRA EQLRIAQEAA DAQKAIADAL AKEAENNNNS GGDNSSDDKG TGSSDIGSWG PFAAIAA II AAIAAIFPFL SGIVKF

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: 7.5
Component:
ConcentrationFormulaName
50.0 mMHepes4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
150.0 mMNaClsodium chloride
1.0 mMMgCl2magnesium chloride

Details: 50 mM HEPES pH=7.5, 150 mM NaCl, 1 mM MgCl2
GridModel: Quantifoil R2/2 / Material: COPPER/RHODIUM / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV
Details: Absorption for 20 sec and blotted for 2.5 sec with blot force -5..
DetailsPurified Surface Layer of Corynebacterium glutamicum composed of PS2 protein

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 31 / Average exposure time: 3.28 sec. / 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 magnification: 96000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 96000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3763
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 16.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.1) / Number images used: 539
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.1)
FSC plot (resolution estimation)

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