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- EMDB-17222: Structure of the FloA-NfeD complex -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-17222
TitleStructure of the FloA-NfeD complex
Map dataCryoEM map of the S.aureus FloA- NfeD complex
Sample
  • Complex: FloA- NfeD complex
    • Protein or peptide: FloA-NfeD complex
    • Protein or peptide: FloA-NfeD complex
Keywordssmall membrane protein / chapperone / lipid rafts / antibiotic resistance / staphylococcus / membrane microdomains / MEMBRANE PROTEIN
Function / homology
Function and homology information


membrane raft / membrane / plasma membrane
Similarity search - Function
Flotillin-like protein FloA / Flotillin-like protein FloA / NfeD-like, C-terminal domain / NfeD-like C-terminal, partner-binding / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
NfeD-like C-terminal domain-containing protein / Flotillin-like protein FloA
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus N315 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.9 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- NfeD complex
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_17222.png

Downloads & links

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Map

FileDownload / File: emd_17222.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of the S.aureus FloA- NfeD complex
Voxel sizeX=Y=Z: 0.58 Å
Density
Contour LevelBy AUTHOR: 0.0188
Minimum - Maximum-0.03104582 - 0.32023406
Average (Standard dev.)-0.00008741991 (±0.0043999823)
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 B

Fileemd_17222_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_17222_half_map_2.map
Annotationhalf map A
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- NfeD complex

EntireName: FloA- NfeD complex
Components
  • Complex: FloA- NfeD complex
    • Protein or peptide: FloA-NfeD complex
    • Protein or peptide: FloA-NfeD complex

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Supramolecule #1: FloA- NfeD complex

SupramoleculeName: FloA- NfeD complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: FloA-NfeD complex, the resolved region covers PHB and coiled-coil domain of FloA and the OB fold domain of NfeD
Source (natural)Organism: Staphylococcus aureus subsp. aureus N315 (bacteria)
Molecular weightTheoretical: 70 KDa

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Macromolecule #1: FloA-NfeD complex

MacromoleculeName: FloA-NfeD complex / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Staphylococcus aureus subsp. aureus N315 (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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Macromolecule #2: FloA-NfeD complex

MacromoleculeName: FloA-NfeD complex / type: protein_or_peptide / ID: 2 / Enantiomer: DEXTRO
Source (natural)Organism: Staphylococcus aureus subsp. aureus N315 (bacteria)
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MSYNNFLQMT TILESTAGDT WVEQVSNIIV QPIFTLILTC LTFLGFVYQL YSKKINAAGI IATLSLLILF LGFLIQGNVN MHSILIFSIG VILVVIELFV VGAVIGIIGM ILITINITTL GDNLLFMLAN VIVALILTIV EWVILVKIFN RKIPFLDKVI LKDSTNSESG ...String:
MSYNNFLQMT TILESTAGDT WVEQVSNIIV QPIFTLILTC LTFLGFVYQL YSKKINAAGI IATLSLLILF LGFLIQGNVN MHSILIFSIG VILVVIELFV VGAVIGIIGM ILITINITTL GDNLLFMLAN VIVALILTIV EWVILVKIFN RKIPFLDKVI LKDSTNSESG YNSHDNRSHL VGKTAQTVTD LRPAGIIFCE NERIDAVSDG NFILRNKTVK ILEVEGTRVV VREVD

UniProtKB: NfeD-like C-terminal domain-containing protein

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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

Concentration0.15 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMTrisTris
300.0 mMNaClSodium chlorideNaClSodium chloride
0.05 %DDMDDM
GridModel: UltrAuFoil R2/2 / Material: GOLD / Mesh: 300 / 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, and full leght NfeD coexpressed

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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: 7.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.0.0) / Software - details: Scipion / Number images used: 40774
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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