[English] 日本語
Yorodumi
- PDB-9qsy: Cryo-EM structure of aquaporin 3 at pH 5.5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9qsy
TitleCryo-EM structure of aquaporin 3 at pH 5.5
ComponentsAquaporin-3
KeywordsMEMBRANE PROTEIN / glycerol channel / hydrogen peroxide transport / tetramer
Function / homology
Function and homology information


positive regulation of immune system process / renal water absorption / Passive transport by Aquaporins / glycerol channel activity / urea transmembrane transporter activity / glycerol transmembrane transport / regulation of keratinocyte differentiation / water transport / water channel activity / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin ...positive regulation of immune system process / renal water absorption / Passive transport by Aquaporins / glycerol channel activity / urea transmembrane transporter activity / glycerol transmembrane transport / regulation of keratinocyte differentiation / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsHuang, P. / Venskutonyte, R. / Lindkvist-Petersson, K.
Funding support Sweden, 3items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aquaporin-3
B: Aquaporin-3
C: Aquaporin-3
D: Aquaporin-3


Theoretical massNumber of molelcules
Total (without water)129,5864
Polymers129,5864
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein
Aquaporin-3 / AQP-3 / Aquaglyceroporin-3


Mass: 32396.549 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AQP3 / Production host: Komagataella pastoris (fungus) / References: UniProt: Q92482
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Aquaporin 3 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Komagataella pastoris (fungus)
Buffer solutionpH: 5.5
Details: 20mM Tris-HCL (pH 8), 100mM Nacl with adjusted pH by MES buffer (pH 5.5)
SpecimenConc.: 7.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

-
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: 2000 nm / Nominal defocus min: 800 nm
Image recordingAverage exposure time: 1.8 sec. / Electron dose: 52.825 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 11820

-
Processing

EM software
IDNameVersionCategory
2PHENIX1.21.2_5419model refinement
13cryoSPARC43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 311941 / Symmetry type: POINT
RefinementHighest resolution: 3.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037800
ELECTRON MICROSCOPYf_angle_d0.48610668
ELECTRON MICROSCOPYf_dihedral_angle_d3.5421060
ELECTRON MICROSCOPYf_chiral_restr0.041220
ELECTRON MICROSCOPYf_plane_restr0.0051340

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more