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- PDB-11wr: Cryo-EM structure of Candida albicans fluoride channel FEX in com... -

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Basic information

Entry
Database: PDB / ID: 11wr
TitleCryo-EM structure of Candida albicans fluoride channel FEX in complex with Fab fragment in LiCl
Components
  • 10E8v4 Fab Heavy Chain
  • 10E8v4 Fab Light Chain
  • Transmembrane protein gp41,Fluoride export protein 1
KeywordsMEMBRANE PROTEIN / Fluoride channel / Fluoride exporter / FEX / Candida albicans / lithium
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 / symbiont-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane ...fluoride transmembrane transport / fluoride transmembrane transporter activity / Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / symbiont-mediated perturbation of host defense response / 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 / membrane / identical protein binding / 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 speciesHomo sapiens (human)
HIV-1 M:B_MN (virus)
Candida albicans (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.56 Å
AuthorsKang, C.-Y. / Stockbridge, R.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM128768 United States
CitationJournal: To Be Published
Title: The structural mechanism of fluoride channel inhibition by lithium in eukaryotes
Authors: Kang, C.-Y. / Heidari, S. / Kolb, S. / An, M. / Ohi, M.D. / Torabifard, H. / Stockbridge, R.B.
History
DepositionMar 16, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 10E8v4 Fab Heavy Chain
B: 10E8v4 Fab Light Chain
C: Transmembrane protein gp41,Fluoride export protein 1


Theoretical massNumber of molelcules
Total (without water)86,3203
Polymers86,3203
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Antibody 10E8v4 Fab Heavy Chain


Mass: 25050.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): ExpiCHO-S cell line / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody 10E8v4 Fab Light Chain


Mass: 22458.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): ExpiCHO-S cell lines / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein Transmembrane protein gp41,Fluoride export protein 1


Mass: 38810.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 M:B_MN (virus), (gene. exp.) Candida albicans (yeast)
Strain: group M subtype B isolate MN, SC5314 / Gene: env, FEX1, CAALFM_C700270WA, CaO19.7095, orf19.7095 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BJ2168 / References: UniProt: P05877, UniProt: Q5AFH3
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeDetails (eV)Entity IDParent-IDSource
1A complex of FEX with 10E8v4 FabCOMPLEXFEX/10E8v4 Fab complex was prepared in LiCl buffer.all0MULTIPLE SOURCES
2FEXCOMPLEX#31RECOMBINANT
310E8v4 FabCOMPLEX#1-#21RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
22Candida albicans (yeast)237561SC5314
32HIV-1 M:B_MN (virus)11696group M subtype B isolate MN
43Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrainCell
22Saccharomyces cerevisiae (brewer's yeast)4932BJ2168
33Cricetulus griseus (Chinese hamster)10029ExpiCHO-S cell line
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2150 mMLithium ChlorideLiCl1
35 mMSodium FluorideNaF1
40.5 mMDDMC24H46O111
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 291.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 1.9 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.2particle selection
2SerialEM4.1.1image acquisition
4cryoSPARC4.6.2CTF correction
7Coot0.9.8.93model fitting
9PHENIX1.21_5207model refinement
10cryoSPARC4.6.2initial Euler assignment
11cryoSPARC4.6.2final Euler assignment
13cryoSPARC4.6.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 112190 / Symmetry type: POINT
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeChain-IDInitial refinement model-ID
15IQ9

5iq9

A5IQ9A1
25IQ9

5iq9

B5IQ9B1
39OP1

9op1

C9OP1C2
RefinementHighest resolution: 3.56 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0045994
ELECTRON MICROSCOPYf_angle_d0.6558160
ELECTRON MICROSCOPYf_dihedral_angle_d5.028827
ELECTRON MICROSCOPYf_chiral_restr0.043925
ELECTRON MICROSCOPYf_plane_restr0.0041021

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