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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: To Be Published
Title: The molecular basis of sodium-dependent fluoride export by the eukaryotic fluoride channel FEX
Authors: Kang C-Y / An MJ / Ohi MD / Stockbridge RB
History
DepositionMay 16, 2025-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 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

Projections

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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
Projections & Slices
AxesZYX

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Slices (1/2)
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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
Projections & Slices
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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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