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- EMDB-70677: Cryo-EM structure of Candida albicans fluoride channel FEX in com... -

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Basic information

Entry
Database: EMDB / ID: EMD-70677
TitleCryo-EM structure of Candida albicans fluoride channel FEX in complex with Fab fragment
Map data
Sample
  • Complex: A complex of FEX with 10E8v4 Fab
    • Complex: FEX
      • Protein or peptide: Transmembrane protein gp41,Fluoride export protein 1
    • Complex: 10E8v4 Fab
      • Protein or peptide: 10E8v4 Fab Heavy Chian
      • Protein or peptide: 10E8v4 Fab Light Chain
KeywordsFluoride channel / Fluoride exporter / FEX / MEMBRANE PROTEIN
Function / homology
Function and homology information


fluoride transmembrane transport / fluoride transmembrane transporter activity / Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane ...fluoride transmembrane transport / fluoride transmembrane transporter activity / Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / identical protein binding / membrane / plasma membrane
Similarity search - Function
Putative fluoride ion transporter CrcB / CrcB-like protein, Camphor Resistance (CrcB) / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160 / Fluoride export protein 1
Similarity search - Component
Biological speciesCandida albicans (yeast) / Homo sapiens (human) / Candida albicans SC5314 (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.05 Å
AuthorsKang C-Y / An MJ / Ohi MD / Stockbridge RB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM128768 United States
CitationJournal: Nat Commun / Year: 2025
Title: The molecular mechanism of fluoride export by the eukaryotic fluoride channel FEX.
Authors: Chia-Yu Kang / Minjun An / Sahar Heidari / Hedieh Torabifard / Melanie D Ohi / Randy B Stockbridge /
Abstract: Much of life on Earth, including plants, fungi, and bacteria, evolved to resist toxic environmental fluoride. In eukaryotes, the major resistance mechanism is fluoride export by membrane proteins ...Much of life on Earth, including plants, fungi, and bacteria, evolved to resist toxic environmental fluoride. In eukaryotes, the major resistance mechanism is fluoride export by membrane proteins known as FEX. Using electrophysiology and transport assays, we establish that FEX from plants and yeasts are highly selective fluoride channels. Fluoride transport activity depends on reversible sodium ion binding, but sodium itself is not transported. We determine a structure of a FEX protein, from pathogenic yeast Candida albicans, using cryo-EM. Bolstered by mutagenesis studies, this structure reveals a fluoride permeation route through a single phenylalanine-lined pore. Molecular dynamics simulations demonstrate that a cation binding motif adjacent to the pore provides a stable sodium binding site that is accessible from the external aqueous solution. Comparison to the structurally related bacterial fluoride channels, Flucs, provides a glimpse of the evolution of structural and mechanistic complexity in a membrane protein family with inverted repeat architecture.
History
DepositionMay 16, 2025-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70677.png

Downloads & links

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Map

FileDownload / File: emd_70677.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 352 pix.
= 293.568 Å		0.83 Å/pix.
x 352 pix.
= 293.568 Å		0.83 Å/pix.
x 352 pix.
= 293.568 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.099
Minimum - Maximum-0.7708014 - 0.95823455
Average (Standard dev.)0.00014806245 (±0.013944275)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 293.568 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70677_msk_1.map
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Additional map: #1

Fileemd_70677_additional_1.map
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Half map: #2

Fileemd_70677_half_map_1.map
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Half map: #1

Fileemd_70677_half_map_2.map
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Sample components

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Entire : A complex of FEX with 10E8v4 Fab

EntireName: A complex of FEX with 10E8v4 Fab
Components
  • Complex: A complex of FEX with 10E8v4 Fab
    • Complex: FEX
      • Protein or peptide: Transmembrane protein gp41,Fluoride export protein 1
    • Complex: 10E8v4 Fab
      • Protein or peptide: 10E8v4 Fab Heavy Chian
      • Protein or peptide: 10E8v4 Fab Light Chain

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Supramolecule #1: A complex of FEX with 10E8v4 Fab

SupramoleculeName: A complex of FEX with 10E8v4 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: FEX

SupramoleculeName: FEX / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Candida albicans (yeast) / Strain: SC5314

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Supramolecule #3: 10E8v4 Fab

SupramoleculeName: 10E8v4 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 10E8v4 Fab Heavy Chian

MacromoleculeName: 10E8v4 Fab Heavy Chian / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.050922 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: EVRLVESGGG LVKPGGSLRL SCSASGFDFD NAWMTWVRQP PGKGLEWVGR ITGPGEGWSV DYAESVKGRF TISRDNTKNT LYLEMNNVR TEDTGYYFCA RTGKYYDFWS GYPPGEEYFQ DWGQGTLVIV SSASTKGPSV FPLAPSSKST SGGTAALGCL V KDYFPEPV ...String:
EVRLVESGGG LVKPGGSLRL SCSASGFDFD NAWMTWVRQP PGKGLEWVGR ITGPGEGWSV DYAESVKGRF TISRDNTKNT LYLEMNNVR TEDTGYYFCA RTGKYYDFWS GYPPGEEYFQ DWGQGTLVIV SSASTKGPSV FPLAPSSKST SGGTAALGCL V KDYFPEPV TVSWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKK VEPK

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Macromolecule #2: 10E8v4 Fab Light Chain

MacromoleculeName: 10E8v4 Fab Light Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.458945 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: SELTQDPAVS VALKQTVTIT CRGDSLRSHY ASWYQKKPGQ APVLLFYGKN NRPSGIPDRF SGSASGNRAS LTITGAQAED EADYYCSSR DKSGSRLSVF GGGTKLTVLS QPKAAPSVTL FPPSSEELQA NKATLVCLIS DFYPGAVTVA WKADSSPVKA G VETTTPSK ...String:
SELTQDPAVS VALKQTVTIT CRGDSLRSHY ASWYQKKPGQ APVLLFYGKN NRPSGIPDRF SGSASGNRAS LTITGAQAED EADYYCSSR DKSGSRLSVF GGGTKLTVLS QPKAAPSVTL FPPSSEELQA NKATLVCLIS DFYPGAVTVA WKADSSPVKA G VETTTPSK QSNNKYAASS YLSLTPEQWK SHRSYSCQVT HEGSTVEKTV AP

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Macromolecule #3: Transmembrane protein gp41,Fluoride export protein 1

MacromoleculeName: Transmembrane protein gp41,Fluoride export protein 1 / type: protein_or_peptide / ID: 3
Details: C. albicans Fluoride export protein 1, N-terminal epitope tag from HIV Transmembrane protein gp41,C. albicans Fluoride export protein 1, N-terminal epitope tag from HIV Transmembrane protein gp41
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Candida albicans SC5314 (yeast) / Strain: SC5314
Molecular weightTheoretical: 38.810254 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: GGLWNWFDIT NWLWYIKNLL NIVHGAIWGV LVRKGLMSLT TYSGSFLSGV IWANFAACVV MGLAIDGEVF WIRLLEEKDY PNKGAIPVY TGLTTGFCGT VSSFSSVILE AFNKAADTDI GVRHHYPNGA YGIMQFLAVI LAQFGLSIMG FHMGKQFSAV V DNYLPLVT ...String:
GGLWNWFDIT NWLWYIKNLL NIVHGAIWGV LVRKGLMSLT TYSGSFLSGV IWANFAACVV MGLAIDGEVF WIRLLEEKDY PNKGAIPVY TGLTTGFCGT VSSFSSVILE AFNKAADTDI GVRHHYPNGA YGIMQFLAVI LAQFGLSIMG FHMGKQFSAV V DNYLPLVT KRIYKVLELT SMILGVVLVV ITCILIGVKK QGSWRSWTFS MLFAPFGALL RYYLSKFLNN KVSNFPLGTF TA NFLGTLL LAVFTLLARG KLPGGKGHIV TNTIALHVLE GLDDGFCGGL TTVSTFVVEL FGLKTLFSYR YGTISILVCF AGV VLILGS YNWSVGLGGE NLYFQSGSAW SHPQFEK

UniProtKB: Envelope glycoprotein gp160, Fluoride export protein 1

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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

Concentration3.8 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
150.0 mMNaClSodium Chloride
5.0 mMNaFSodium Fluoride
0.5 mMC24H46O11DDM
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 1.9 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.5) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: AlphaFold2 predicted model for FEX Protein and PDB 5IQ9 for 10E8v4 Fab
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.05 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Number images used: 164326
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5) / Details: non-uniform refinement
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
ChainDetailsPDB ID
chain_id: c, source_name: AlphaFold, initial_model_type: in silico modelUse AlphaFold2 to generate the FEX model.
source_name: PDB, initial_model_type: experimental model

5iq9

Output model

PDB-9op1:
Cryo-EM structure of Candida albicans fluoride channel FEX in complex with Fab fragment

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