+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17233 | |||||||||
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Title | Structure of the FloA-NfeD complex with Pbp2a pray bound | |||||||||
Map data | FloA-NfeD dimer with the client protein bound | |||||||||
Sample |
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Keywords | small membrane protein / chapperone / lipid rafts / antibiotic resistance / staphylococcus / membrane microdomains / MEMBRANE PROTEIN | |||||||||
Function / homology | Flotillin-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 species | Staphylococcus aureus subsp. aureus N315 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.1 Å | |||||||||
Authors | Ukleja 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
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17233.map.gz | 61.5 MB | EMDB map data format | |
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Header (meta data) | emd-17233-v30.xml emd-17233.xml | 20.8 KB 20.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17233_fsc.xml | 14.8 KB | Display | FSC data file |
Images | emd_17233.png | 51.8 KB | ||
Filedesc metadata | emd-17233.cif.gz | 5.9 KB | ||
Others | emd_17233_additional_1.map.gz emd_17233_half_map_1.map.gz emd_17233_half_map_2.map.gz | 63.3 MB 116 MB 116 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17233 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17233 | HTTPS FTP |
-Validation report
Summary document | emd_17233_validation.pdf.gz | 817.5 KB | Display | EMDB validaton report |
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Full document | emd_17233_full_validation.pdf.gz | 817.1 KB | Display | |
Data in XML | emd_17233_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | emd_17233_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17233 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17233 | HTTPS FTP |
-Related structure data
Related structure data | 17230 |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_17233.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | FloA-NfeD dimer with the client protein bound | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.65 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: client protein Pbp2a map
File | emd_17233_additional_1.map | ||||||||||||
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Annotation | client protein Pbp2a map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B
File | emd_17233_half_map_1.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map A
File | emd_17233_half_map_2.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : FloA- NfeD dimer bound to Pbp2a
Entire | Name: FloA- NfeD dimer bound to Pbp2a |
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Components |
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-Supramolecule #1: FloA- NfeD dimer bound to Pbp2a
Supramolecule | Name: 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 |
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Source (natural) | Organism: Staphylococcus aureus subsp. aureus N315 (bacteria) |
Molecular weight | Theoretical: 200 KDa |
-Macromolecule #1: Flotillin-like protein FloA
Macromolecule | Name: Flotillin-like protein FloA / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO |
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Source (natural) | Organism: Staphylococcus aureus subsp. aureus N315 (bacteria) |
Sequence | String: 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 |
-Macromolecule #2: Flotilin associated protein-NfeD
Macromolecule | Name: Flotilin associated protein-NfeD / type: protein_or_peptide / ID: 2 / Enantiomer: DEXTRO |
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Source (natural) | Organism: Staphylococcus aureus subsp. aureus N315 (bacteria) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: 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 | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV | ||||||||||||
Details | Full lenght FloA- NfeD complex bound to unfolded Pbp2a |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 12340 / Average electron dose: 47.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 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 stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Refinement | Protocol: FLEXIBLE FIT |