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- EMDB-17231: Structure of the FloA-NfeD dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-17231
TitleStructure of the FloA-NfeD dimer
Map dataCryo EM map of the FloA-NfeD heterodimer
Sample
  • Complex: FloA- NfeD dimer
    • Protein or peptide: FloA- flotilin linke protein
    • Protein or peptide: flotilin associated protein NfeD
Keywordssmall membrane protein / chapperone / lipid rafts / antibiotic resistance / staphylococcus / membrane microdomains / MEMBRANE PROTEIN
Function / homology
Function and homology information


membrane raft / plasma membrane
Similarity search - Function
Flotillin-like protein FloA / Flotillin-like protein FloA / NfeD-like, C-terminal domain / : / NfeD-like C-terminal, partner-binding domain / 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: 8.8 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 the S.aureus FloA-NdeD dimer
Authors: 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
History
DepositionApr 27, 2023-
Header (metadata) releaseJun 19, 2024-
Map releaseJun 19, 2024-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17231.png

Downloads & links

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Map

FileDownload / File: emd_17231.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo EM map of the FloA-NfeD heterodimer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 180 pix.
= 181.944 Å		1.01 Å/pix.
x 180 pix.
= 181.944 Å		1.01 Å/pix.
x 180 pix.
= 181.944 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0108 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0463
Minimum - Maximum-0.22076888 - 0.74340314
Average (Standard dev.)0.0014728665 (±0.0100140115)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 181.944 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map B

Fileemd_17231_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_17231_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 dimer

EntireName: FloA- NfeD dimer
Components
  • Complex: FloA- NfeD dimer
    • Protein or peptide: FloA- flotilin linke protein
    • Protein or peptide: flotilin associated protein NfeD

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Supramolecule #1: FloA- NfeD dimer

SupramoleculeName: FloA- NfeD dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: S.aureus FloA protein in complex with NfeD, forming a heterotetramer (dier of heterodimers)
Source (natural)Organism: Staphylococcus aureus subsp. aureus N315 (bacteria)
Molecular weightTheoretical: 140 KDa

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Macromolecule #1: FloA- flotilin linke protein

MacromoleculeName: FloA- flotilin linke protein / 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: flotilin associated protein NfeD

MacromoleculeName: flotilin associated protein NfeD / type: protein_or_peptide / ID: 2 / Enantiomer: DEXTRO
Source (natural)Organism: Staphylococcus aureus subsp. aureus N315 (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

Concentration0.1 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMTrisTris
300.0 mMNaClNaCl
5.0 %glycerolglycerol
GridModel: UltrAuFoil R2/2 / Material: GOLD / Mesh: 300 / 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- NfeD complex

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 19615 / Average electron dose: 47.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 165000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3706679
Startup modelType of model: OTHER / Details: ab iniito model from cryoSPARC
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 8.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.0.0) / Number images used: 48648
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: FLEXIBLE FIT

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