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- EMDB-39063: Cryo-EM structure of GlpF with P177 deletion in POPC nanodisc -

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Basic information

Entry
Database: EMDB / ID: EMD-39063
TitleCryo-EM structure of GlpF with P177 deletion in POPC nanodisc
Map data
Sample
  • Complex: Tetramer of GlpF with P177 deletion in POPC nanodisc
    • Protein or peptide: Glycerol uptake facilitator protein
Keywordswater channel / aquaporin / aquaglyceroporin / glycerol / MEMBRANE PROTEIN
Function / homology
Function and homology information


glycerol transmembrane transporter activity / glycerol channel activity / glycerol transmembrane transport / cellular response to mercury ion / plasma membrane
Similarity search - Function
: / Major intrinsic protein, conserved site / MIP family signature. / Major intrinsic protein / Major intrinsic protein / Aquaporin-like
Similarity search - Domain/homology
Glycerol uptake facilitator protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.26 Å
AuthorsKozai D / Suzuki S / Kamegawa A / Nishikawa K / Suzuki H / Fujiyoshi Y
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20H00451 Japan
Japan Agency for Medical Research and Development (AMED)JP21ae0121028 Japan
CitationJournal: Nat Commun / Year: 2025
Title: Narrowed pore conformations of aquaglyceroporins AQP3 and GlpF.
Authors: Daisuke Kozai / Masao Inoue / Shota Suzuki / Akiko Kamegawa / Kouki Nishikawa / Hiroshi Suzuki / Toru Ekimoto / Mitsunori Ikeguchi / Yoshinori Fujiyoshi /
Abstract: Aquaglyceroporins such as aquaporin-3 (AQP3) and its bacterial homologue GlpF facilitate water and glycerol permeation across lipid bilayers. X-ray crystal structures of GlpF showed open pore ...Aquaglyceroporins such as aquaporin-3 (AQP3) and its bacterial homologue GlpF facilitate water and glycerol permeation across lipid bilayers. X-ray crystal structures of GlpF showed open pore conformations, and AQP3 has also been predicted to adopt this conformation. Here we present cryo-electron microscopy structures of rat AQP3 and GlpF in different narrowed pore conformations. In n-dodecyl-β-D-maltopyranoside detergent micelles, aromatic/arginine constriction filter residues of AQP3 containing Tyr212 form a 2.8-Å diameter pore, whereas in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) nanodiscs, Tyr212 inserts into the pore. Molecular dynamics simulation shows the Tyr212-in conformation is stable and largely suppresses water permeability. AQP3 reconstituted in POPC liposomes exhibits water and glycerol permeability, suggesting that the Tyr212-in conformation may be altered during permeation. AQP3 Y212F and Y212T mutant structures suggest that the aromatic residue drives the pore-inserted conformation. The aromatic residue is conserved in AQP7 and GlpF, but neither structure exhibits the AQP3-like conformation in POPC nanodiscs. Unexpectedly, the GlpF pore is covered by an intracellular loop, but the loop is flexible and not primarily related to the GlpF permeability. Our findings illuminate the unique AQP3 conformation and structural diversity of aquaglyceroporins.
History
DepositionFeb 6, 2024-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39063.png

Downloads & links

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Map

FileDownload / File: emd_39063.map.gz / Format: CCP4 / Size: 11.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 146 pix.
= 146.73 Å		1.01 Å/pix.
x 146 pix.
= 146.73 Å		1.01 Å/pix.
x 146 pix.
= 146.73 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.005 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.63
Minimum - Maximum-2.6226711 - 3.8499298
Average (Standard dev.)0.0014633407 (±0.1967676)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions146146146
Spacing146146146
CellA=B=C: 146.73 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39063_msk_1.map
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Half map: #2

Fileemd_39063_half_map_1.map
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Half map: #1

Fileemd_39063_half_map_2.map
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Sample components

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Entire : Tetramer of GlpF with P177 deletion in POPC nanodisc

EntireName: Tetramer of GlpF with P177 deletion in POPC nanodisc
Components
  • Complex: Tetramer of GlpF with P177 deletion in POPC nanodisc
    • Protein or peptide: Glycerol uptake facilitator protein

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Supramolecule #1: Tetramer of GlpF with P177 deletion in POPC nanodisc

SupramoleculeName: Tetramer of GlpF with P177 deletion in POPC nanodisc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Glycerol uptake facilitator protein

MacromoleculeName: Glycerol uptake facilitator protein / type: protein_or_peptide / ID: 1 / Details: 2-9 His tag 14-19 thrombin digestion site / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 31.8201 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHHHA AAGLVPRGSM SQTSTLKGQC IAEFLGTGLL IFFGVGCVAA LKVAGASFGQ WEISVIWGLG VAMAIYLTAG VSGAHLNPA VTIALWLFAC FDKRKVIPFI VSQVAGAFCA AALVYGLYYN LFFDFEQTHH IVRGSVESVD LAGTFSTYPN P HINFVQAF ...String:
MHHHHHHHHA AAGLVPRGSM SQTSTLKGQC IAEFLGTGLL IFFGVGCVAA LKVAGASFGQ WEISVIWGLG VAMAIYLTAG VSGAHLNPA VTIALWLFAC FDKRKVIPFI VSQVAGAFCA AALVYGLYYN LFFDFEQTHH IVRGSVESVD LAGTFSTYPN P HINFVQAF AVEMVITAIL MGLILALTDD GNGVPRGLAP LLIGLLIAVI GASMGPLTGF AMNPARDFGP KVFAWLAGWG NV AFTGGRD IPYFLVPLFG PIVGAIVGAF AYRKLIGRHL PCDICVVEEK ETTTPSEQKA SL

UniProtKB: Glycerol uptake facilitator protein

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 63.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.26 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 462907
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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