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- EMDB-39060: Cryo-EM structure of AQP7 in POPC nanodisc -

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Basic information

Entry
Database: EMDB / ID: EMD-39060
TitleCryo-EM structure of AQP7 in POPC nanodisc
Map datamain
Sample
  • Organelle or cellular component: Tetramer of AQP7 in POPC nanodisc
    • Protein or peptide: Green fluorescent protein,Aquaporin-7
  • Ligand: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
Keywordswater channel / aquaporin / aquaglyceroporin / glycerol / MEMBRANE PROTEIN
Function / homology
Function and homology information


Transport of glycerol from adipocytes to the liver by Aquaporins / Passive transport by Aquaporins / glycerol channel activity / urea transmembrane transporter activity / glycerol transmembrane transport / water transport / water channel activity / lipid droplet / cytoplasmic vesicle membrane / bioluminescence ...Transport of glycerol from adipocytes to the liver by Aquaporins / Passive transport by Aquaporins / glycerol channel activity / urea transmembrane transporter activity / glycerol transmembrane transport / water transport / water channel activity / lipid droplet / cytoplasmic vesicle membrane / bioluminescence / generation of precursor metabolites and energy / cell-cell junction / basolateral plasma membrane / plasma membrane / cytoplasm
Similarity search - Function
: / Major intrinsic protein / Major intrinsic protein / Aquaporin-like / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
Aquaporin-7 / Green fluorescent protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.49 Å
AuthorsKozai D / Suzuki S / Kamegawa A / Nishikawa K / Suzuki H / Fujiyosh 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-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39060.png

Downloads & links

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Map

FileDownload / File: emd_39060.map.gz / Format: CCP4 / Size: 8.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 130 pix.
= 130.65 Å		1.01 Å/pix.
x 130 pix.
= 130.65 Å		1.01 Å/pix.
x 130 pix.
= 130.65 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: 0.413
Minimum - Maximum-2.0099378 - 2.9257782
Average (Standard dev.)0.0012817378 (±0.18818398)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions130130130
Spacing130130130
CellA=B=C: 130.65 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39060_msk_1.map
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Half map: half a

Fileemd_39060_half_map_1.map
Annotationhalf a
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Half map: half b

Fileemd_39060_half_map_2.map
Annotationhalf b
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Sample components

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Entire : Tetramer of AQP7 in POPC nanodisc

EntireName: Tetramer of AQP7 in POPC nanodisc
Components
  • Organelle or cellular component: Tetramer of AQP7 in POPC nanodisc
    • Protein or peptide: Green fluorescent protein,Aquaporin-7
  • Ligand: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine

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Supramolecule #1: Tetramer of AQP7 in POPC nanodisc

SupramoleculeName: Tetramer of AQP7 in POPC nanodisc / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Green fluorescent protein,Aquaporin-7

MacromoleculeName: Green fluorescent protein,Aquaporin-7 / type: protein_or_peptide / ID: 1
Details: 5-12 His tag 13-251 GFP tag,255-261 TEV protease digestion site
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 67.259117 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGSSHHHHHH HHMVSKGEEL FTGVVPILVE LDGDVNGHKF SVSGEGEGDA TYGKLTLKFI CTTGKLPVPW PTLVTTLTYG VQCFSRYPD HMKQHDFFKS AMPEGYVQER TIFFKDDGNY KTRAEVKFEG DTLVNRIELK GIDFKEDGNI LGHKLEYNYN S HNVYIMAD ...String:
MGSSHHHHHH HHMVSKGEEL FTGVVPILVE LDGDVNGHKF SVSGEGEGDA TYGKLTLKFI CTTGKLPVPW PTLVTTLTYG VQCFSRYPD HMKQHDFFKS AMPEGYVQER TIFFKDDGNY KTRAEVKFEG DTLVNRIELK GIDFKEDGNI LGHKLEYNYN S HNVYIMAD KQKNGIKVNF KIRHNIEDGS VQLADHYQQN TPIGDGPVLL PDNHYLSTQS KLSKDPNEKR DHMVLLEFVT AA GITLGMD ELYKSSGENL YFQGHMASMV QASGHRRSTR GSKMVSWSVI AKIQEILQRK MVREFLAEFM STYVMMVFGL GSV AHMVLN KKYGSYLGVN LGFGFGVTMG VHVAGRISGA HMNAAVTFAN CALGRVPWRK FPVYVLGQFL GSFLAAATIY SLFY TAILH FSGGQLMVTG PVATAGIFAT YLPDHMTLWR GFLNEAWLTG MLQLCLFAIT DQENNPALPG TEALVIGILV VIIGV SLGM NTGYAINPSR DLPPRIFTFI AGWGKQVFSN GENWWWVPVV APLLGAYLGG IIYLVFIGST IPREPLKLED SVAYED HGI TVLPKMGSHE PTISPLTPVS VSPANRSSVH PAPPLHESMA LEHF

UniProtKB: Green fluorescent protein, Aquaporin-7

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Macromolecule #2: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phospho...

MacromoleculeName: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
type: ligand / ID: 2 / Number of copies: 1 / Formula: P5S
Molecular weightTheoretical: 792.075 Da
Chemical component information

ChemComp-P5S:
O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 65.3 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: INSILICO MODEL / In silico model: AlphaFold
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.49 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 148023
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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