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- EMDB-17233: Structure of the FloA-NfeD complex with Pbp2a pray bound -

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Basic information

Entry
Database: EMDB / ID: EMD-17233
TitleStructure of the FloA-NfeD complex with Pbp2a pray bound
Map dataFloA-NfeD dimer with the client protein bound
Sample
  • Complex: FloA- NfeD dimer bound to Pbp2a
    • Protein or peptide: Flotillin-like protein FloA
    • Protein or peptide: Flotilin associated protein-NfeD
Keywordssmall membrane protein / chapperone / lipid rafts / antibiotic resistance / staphylococcus / membrane microdomains / MEMBRANE PROTEIN
Function / homologyFlotillin-like protein FloA / Flotillin-like protein FloA / NfeD-like, C-terminal domain / NfeD-like C-terminal, partner-binding / membrane raft / Nucleic acid-binding, OB-fold / plasma membrane / NfeD-like C-terminal domain-containing protein / Flotillin-like protein FloA
Function and homology information
Biological speciesStaphylococcus aureus subsp. aureus N315 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.1 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 complex with Pbp2a
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_17233.png

Downloads & links

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Map

FileDownload / File: emd_17233.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFloA-NfeD dimer with the client protein bound
Voxel sizeX=Y=Z: 0.65 Å
Density
Contour LevelBy AUTHOR: 0.0167
Minimum - Maximum-0.089322075 - 0.69226736
Average (Standard dev.)-0.00009015324 (±0.0042924033)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 208.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: client protein Pbp2a map

Fileemd_17233_additional_1.map
Annotationclient protein Pbp2a map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_17233_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_17233_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 bound to Pbp2a

EntireName: FloA- NfeD dimer bound to Pbp2a
Components
  • Complex: FloA- NfeD dimer bound to Pbp2a
    • Protein or peptide: Flotillin-like protein FloA
    • Protein or peptide: Flotilin associated protein-NfeD

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Supramolecule #1: FloA- NfeD dimer bound to Pbp2a

SupramoleculeName: FloA- NfeD dimer bound to Pbp2a / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: S.aureus FloA protein in complex with NfeD, forming a heterotetramer (dier of heterodimers) bound to unfolded Pbp2a pray protein
Source (natural)Organism: Staphylococcus aureus subsp. aureus N315 (bacteria)
Molecular weightTheoretical: 200 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 aureus subsp. aureus N315 (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 / 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- NfeD complex bound to unfolded Pbp2a

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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: 12340 / 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: 2515827
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: 8.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.0.0)
Details: Local Refinement in cryoSPARC with volume subtraction
Number images used: 52403
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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