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- EMDB-17217: Structure of Staphylococcus aureus FloA protein -

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Basic information

Entry
Database: EMDB / ID: EMD-17217
TitleStructure of Staphylococcus aureus FloA protein
Map dataS.aureus FloA cryo-EM map
Sample
  • Complex: FloA protein monomer
    • Protein or peptide: Flotillin-like protein FloA
Keywordssmall membrane protein / chapperone / lipid rafts / antibiotic resistance / staphylococcus / membrane microdomains / MEMBRANE PROTEIN
Function / homologyFlotillin-like protein FloA / Flotillin-like protein FloA / membrane raft / plasma membrane / Flotillin-like protein FloA
Function and homology information
Biological speciesStaphylococcus aureus subsp. aureus N315 (bacteria) / Staphylococcus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.0 Å
AuthorsUkleja M / Kricks L / Torrens G / Peschiera I / Rodrigues-Lopes I / Krupka M / Garcia Fernandez J / del Campo R / Eulalio A / Mateus A ...Ukleja M / Kricks L / Torrens G / Peschiera I / Rodrigues-Lopes I / Krupka M / Garcia Fernandez J / del Campo R / Eulalio A / Mateus A / Lopez Bravo M / Rico AI / Cava F / Lopez D
Funding support Sweden, Spain, 2 items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Spanish Ministry of Science, Innovation, and Universities Spain
CitationJournal: To Be Published
Title: Structure of Staphylococcus aureus FloA protein
Authors: Ukleja M / Lopez D
History
DepositionApr 26, 2023-
Header (metadata) releaseMay 8, 2024-
Map releaseMay 8, 2024-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17217.png

Downloads & links

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Map

FileDownload / File: emd_17217.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationS.aureus FloA cryo-EM map
Voxel sizeX=Y=Z: 0.58 Å
Density
Contour LevelBy AUTHOR: 0.0237
Minimum - Maximum-0.013969864 - 0.24424292
Average (Standard dev.)0.0011963352 (±0.0053198254)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 185.59999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_17217_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_17217_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : FloA protein monomer

EntireName: FloA protein monomer
Components
  • Complex: FloA protein monomer
    • Protein or peptide: Flotillin-like protein FloA

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Supramolecule #1: FloA protein monomer

SupramoleculeName: FloA protein monomer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: S.aureus FloA protein, full lenght
Source (natural)Organism: Staphylococcus aureus subsp. aureus N315 (bacteria)
Molecular weightTheoretical: 35 KDa

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Macromolecule #1: Flotillin-like protein FloA

MacromoleculeName: Flotillin-like protein FloA / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Staphylococcus (bacteria)
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MFSLSFIVIA VIIIVALLIL FSFVPIGLWI SALAAGVHVG IGTLVGMRLR RVSPRKVIAP LIKAHKAGLA LTTNQLESHY LAGGNVDRVV DANIAAQRAD IDLPFERAAA IDLAGRDVLE AVQMSVNPKV IETPFIAGVA MNGIEVKAKA RITVRANIAR LVGGAGEETI ...String:
MFSLSFIVIA VIIIVALLIL FSFVPIGLWI SALAAGVHVG IGTLVGMRLR RVSPRKVIAP LIKAHKAGLA LTTNQLESHY LAGGNVDRVV DANIAAQRAD IDLPFERAAA IDLAGRDVLE AVQMSVNPKV IETPFIAGVA MNGIEVKAKA RITVRANIAR LVGGAGEETI IARVGEGIVS TIGSSKHHTE VLENPDNISK TVLSKGLDSG TAFEILSIDI ADVDISKNIG ADLQTEQALA DKNIAQAKAE ERRAMAVATE QEMKARVQEM HAKVVEAESE VPLAMAEALR SGNISVKDYY NLKNIEADTG MRNAINKRTD QSDDESPEH

UniProtKB: Flotillin-like protein FloA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMTrisTris
300.0 mMNaClSodium chlorideNaClSodium chloride
0.05 %DDMDDM
GridModel: UltrAuFoil R2/2 / Support film - Material: GOLD / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
DetailsFull lenght FloA

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 215000
Specialist opticsEnergy filter - Slit width: 10 eV
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 9653 / Average exposure time: 2.33 sec. / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 478555
Startup modelType of model: NONE
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC / Software - details: Scipion / Details: ab initio reconstruction protocol from cryoSPARC
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 3.0.0) / Software - details: Scipion / Details: Local refinement in cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.0.0) / Software - details: Scipion / Number images used: 118042
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: cross-correlation criteria

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