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- PDB-8y8n: Cryo-EM structure of AQP3 in DDM micelle -

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Basic information

Entry
Database: PDB / ID: 8y8n
TitleCryo-EM structure of AQP3 in DDM micelle
ComponentsAquaporin-3
KeywordsMEMBRANE PROTEIN / water channel / aquaporin / aquaglyceroporin / glycerol
Function / homology
Function and homology information


positive regulation of immune system process / polyol transmembrane transporter activity / polyol transmembrane transport / Passive transport by Aquaporins / renal water absorption / urea transport / glycerol channel activity / urea transmembrane transporter activity / glycerol transmembrane transport / water transport ...positive regulation of immune system process / polyol transmembrane transporter activity / polyol transmembrane transport / Passive transport by Aquaporins / renal water absorption / urea transport / glycerol channel activity / urea transmembrane transporter activity / glycerol transmembrane transport / water transport / water channel activity / Vasopressin regulates renal water homeostasis via Aquaporins / odontogenesis / response to retinoic acid / response to ischemia / establishment of localization in cell / cell-cell junction / basolateral plasma membrane / cellular response to hypoxia / identical protein binding / 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 speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsKozai, D. / Suzuki, S. / Kamegawa, A. / Nishikawa, K. / Suzuki, H. / Fujiyoshi, Y.
Funding support Japan, 2items
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, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aquaporin-3


Theoretical massNumber of molelcules
Total (without water)33,5231
Polymers33,5231
Non-polymers00
Water00
1
A: Aquaporin-3

A: Aquaporin-3

A: Aquaporin-3

A: Aquaporin-3


Theoretical massNumber of molelcules
Total (without water)134,0924
Polymers134,0924
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation3
SymmetryPoint symmetry: (Schoenflies symbol: C4 (4 fold cyclic))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
2generate(-1), (1), (1)182.16
3generate(-1), (-1), (1)182.16, 182.16
4generate(1), (-1), (1)182.16

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Components

#1: Protein Aquaporin-3 / AQP-3 / 31.4 kDa water channel protein / Aquaglyceroporin-3


Mass: 33522.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 2-9 His tag 14-19 thrombin digestion site / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Aqp3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P47862
Has ligand of interestY
Has protein modificationN

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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

ComponentName: Tetramer of AQP3 in DDM micelle / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 65.3 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 153591 / Symmetry type: POINT
RefinementHighest resolution: 3.12 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0028420
ELECTRON MICROSCOPYf_angle_d0.48111484
ELECTRON MICROSCOPYf_dihedral_angle_d5.4851382
ELECTRON MICROSCOPYf_chiral_restr0.0351332
ELECTRON MICROSCOPYf_plane_restr0.0041428

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