[English] 日本語
Yorodumi
- EMDB-17222: Structure of the FloA-NfeD complex -

+
Open data


ID or keywords:

Loading...

-
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 / 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: 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: Nat Commun / Year: 2024
Title: Flotillin-mediated stabilization of unfolded proteins in bacterial membrane microdomains.
Authors: Marta Ukleja / Lara Kricks / Gabriel Torrens / Ilaria Peschiera / Ines Rodrigues-Lopes / Marcin Krupka / Julia García-Fernández / Roberto Melero / Rosa Del Campo / Ana Eulalio / André ...Authors: Marta Ukleja / Lara Kricks / Gabriel Torrens / Ilaria Peschiera / Ines Rodrigues-Lopes / Marcin Krupka / Julia García-Fernández / Roberto Melero / Rosa Del Campo / Ana Eulalio / André Mateus / María López-Bravo / Ana I Rico / Felipe Cava / Daniel Lopez /
Abstract: The function of many bacterial processes depends on the formation of functional membrane microdomains (FMMs), which resemble the lipid rafts of eukaryotic cells. However, the mechanism and the ...The function of many bacterial processes depends on the formation of functional membrane microdomains (FMMs), which resemble the lipid rafts of eukaryotic cells. However, the mechanism and the biological function of these membrane microdomains remain unclear. Here, we show that FMMs in the pathogen methicillin-resistant Staphylococcus aureus (MRSA) are dedicated to confining and stabilizing proteins unfolded due to cellular stress. The FMM scaffold protein flotillin forms a clamp-shaped oligomer that holds unfolded proteins, stabilizing them and favoring their correct folding. This process does not impose a direct energy cost on the cell and is crucial to survival of ATP-depleted bacteria, and thus to pathogenesis. Consequently, FMM disassembling causes the accumulation of unfolded proteins, which compromise MRSA viability during infection and cause penicillin re-sensitization due to PBP2a unfolding. Thus, our results indicate that FMMs mediate ATP-independent stabilization of unfolded proteins, which is essential for bacterial viability during infection.
History
DepositionApr 26, 2023-
Header (metadata) releaseMay 8, 2024-
Map releaseMay 8, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_17222.png

Downloads & links

-
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
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.58 Å/pix.
x 320 pix.
= 185.6 Å		0.58 Å/pix.
x 320 pix.
= 185.6 Å		0.58 Å/pix.
x 320 pix.
= 185.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.58 Å
Density

Histogram

Histogram (log scale)
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 °

-
Supplemental data

-
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)

-
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)

-
Sample components

-
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

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.15 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMTrisTris
300.0 mMNaClNaCl
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

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 10 eV
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
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: 2.4 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 215000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 478555
Startup modelType of model: NONE
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
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
FSC plot (resolution estimation)

-
Atomic model buiding 1

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more