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- EMDB-53343: Cryo-EM structure of aquaporin 3 at pH 8.0 -

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Basic information

Entry
Database: EMDB / ID: EMD-53343
TitleCryo-EM structure of aquaporin 3 at pH 8.0
Map data
Sample
  • Organelle or cellular component: Aquaporin 3
    • Protein or peptide: Aquaporin-3
  • Ligand: GLYCEROL
  • Ligand: fluorinated fos-choline-8
  • Ligand: water
Keywordsmembrane protein / glycerol channel / hydrogen peroxide transport / tetramer
Function / homology
Function and homology information


positive regulation of immune system process / renal water absorption / glycerol channel activity / Passive transport by Aquaporins / urea transmembrane transporter activity / regulation of keratinocyte differentiation / glycerol transmembrane transport / water transport / water channel activity / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin ...positive regulation of immune system process / renal water absorption / glycerol channel activity / Passive transport by Aquaporins / urea transmembrane transporter activity / regulation of keratinocyte differentiation / glycerol transmembrane transport / water transport / water channel activity / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / response to vitamin D / odontogenesis / response to retinoic acid / renal water homeostasis / response to ischemia / establishment of localization in cell / response to calcium ion / cell-cell junction / Vasopressin regulates renal water homeostasis via Aquaporins / cellular response to hypoxia / basolateral plasma membrane / nucleoplasm / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Aquaporin 3 / : / Major intrinsic protein, conserved site / MIP family signature. / Major intrinsic protein / Major intrinsic protein / Aquaporin-like
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsHuang P / Venskutonyte R / Lindkvist-Petersson K
Funding support Sweden, 3 items
OrganizationGrant numberCountry
Swedish Research Council2022-06230 Sweden
Swedish Research Council2024-02673 Sweden
Cancerfonden23 2746 Pj, 20 0747 PjF Sweden
CitationJournal: Nat Commun / Year: 2025
Title: Structural insights into AQP3 channel closure upon pH and redox changes reveal an autoregulatory molecular mechanism.
Authors: Peng Huang / Raminta Venskutonytė / Carter J Wilson / Sara Bsharat / Rashmi B Prasad / Pontus Gourdon / Isabella Artner / Bert L de Groot / Karin Lindkvist-Petersson /
Abstract: Regulation of intracellular levels of reactive oxygen species (ROS) remains poorly understood. Aquaporin 3 (AQP3) facilitates the membrane transport of hydrogen peroxide (HO), a key ROS signaling ...Regulation of intracellular levels of reactive oxygen species (ROS) remains poorly understood. Aquaporin 3 (AQP3) facilitates the membrane transport of hydrogen peroxide (HO), a key ROS signaling molecule. Here we elucidate the molecular mechanism of AQP3 and show that its regulatory properties are both pH dependent and autoregulated by HO. Using single particle cryo-electron microscopy, we present open and closed conformations of human AQP3. At pH 8.0, the channel adopts an open state, while acidic pH or exposure to HO promotes closure via a large conformational rearrangement of extracellular loop E. These findings reveal a mechanism for autoregulation of HO transport and establish AQP3 as a key modulator of redox homeostasis in human pancreatic β-cells.
History
DepositionApr 7, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53343.png

Downloads & links

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Map

FileDownload / File: emd_53343.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 300 pix.
= 255. Å		0.85 Å/pix.
x 300 pix.
= 255. Å		0.85 Å/pix.
x 300 pix.
= 255. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.8122044 - 1.2257503
Average (Standard dev.)0.0011978485 (±0.029328479)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 255.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_53343_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53343_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Aquaporin 3

EntireName: Aquaporin 3
Components
  • Organelle or cellular component: Aquaporin 3
    • Protein or peptide: Aquaporin-3
  • Ligand: GLYCEROL
  • Ligand: fluorinated fos-choline-8
  • Ligand: water

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Supramolecule #1: Aquaporin 3

SupramoleculeName: Aquaporin 3 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Aquaporin-3

MacromoleculeName: Aquaporin-3 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.396549 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MGRQKELVSR CGEMLHIRYR LLRQALAECL GTLILVMFGC GSVAQVVLSR GTHGGFLTIN LAFGFAVTLG ILIAGQVSGA HLNPAVTFA MCFLAREPWI KLPIYTLAQT LGAFLGAGIV FGLYYDAIWH FADNQLFVSG PNGTAGIFAT YPSGHLDMIN G FFDQFIGT ...String:
MGRQKELVSR CGEMLHIRYR LLRQALAECL GTLILVMFGC GSVAQVVLSR GTHGGFLTIN LAFGFAVTLG ILIAGQVSGA HLNPAVTFA MCFLAREPWI KLPIYTLAQT LGAFLGAGIV FGLYYDAIWH FADNQLFVSG PNGTAGIFAT YPSGHLDMIN G FFDQFIGT ASLIVCVLAI VDPYNNPVPR GLEAFTVGLV VLVIGTSMGF NSGYAVNPAR DFGPRLFTAL AGWGSAVFTT GQ HWWWVPI VSPLLGSIAG VFVYQLMIGC HLEQPPPSNE EENVKLAHVK HKEQIHHHHH H

UniProtKB: Aquaporin-3

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Macromolecule #2: GLYCEROL

MacromoleculeName: GLYCEROL / type: ligand / ID: 2 / Number of copies: 8 / Formula: GOL
Molecular weightTheoretical: 92.094 Da
Chemical component information

ChemComp-GOL:
GLYCEROL

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Macromolecule #3: fluorinated fos-choline-8

MacromoleculeName: fluorinated fos-choline-8 / type: ligand / ID: 3 / Number of copies: 1 / Formula: A1H8K
Molecular weightTheoretical: 530.239 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration2 mg/mL
BufferpH: 8 / Details: 20mM Tris-HCL pH 8, 100 mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average exposure time: 1.7 sec. / Average electron dose: 39.866 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: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 139031
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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