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- PDB-8y8v: Cryo-EM structure of AQP7 in POPC nanodisc -

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Basic information

Entry
Database: PDB / ID: 8y8v
TitleCryo-EM structure of AQP7 in POPC nanodisc
ComponentsGreen fluorescent protein,Aquaporin-7
KeywordsMEMBRANE PROTEIN / water channel / aquaporin / aquaglyceroporin / glycerol
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
Chem-P5S / Aquaporin-7 / Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.49 Å
AuthorsKozai, D. / Suzuki, S. / Kamegawa, A. / Nishikawa, K. / Suzuki, H. / Fujiyosh, 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
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein,Aquaporin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0512
Polymers67,2591
Non-polymers7921
Water00
1
A: Green fluorescent protein,Aquaporin-7
hetero molecules

A: Green fluorescent protein,Aquaporin-7
hetero molecules

A: Green fluorescent protein,Aquaporin-7
hetero molecules

A: Green fluorescent protein,Aquaporin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)272,2058
Polymers269,0364
Non-polymers3,1684
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation3
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: C4 (4 fold cyclic))

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Components

#1: Protein Green fluorescent protein,Aquaporin-7 / AQP-7 / Aquaglyceroporin-7 / Aquaporin adipose / AQPap / Aquaporin-7-like


Mass: 67259.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 5-12 His tag 13-251 GFP tag,255-261 TEV protease digestion site
Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Homo sapiens (human)
Gene: GFP, AQP7, AQP7L, AQP9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P42212, UniProt: O14520
#2: Chemical ChemComp-P5S / O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine / phosphatidyl serine


Mass: 792.075 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H82NO10P / Feature type: SUBJECT OF INVESTIGATION
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 AQP7 in POPC nanodisc / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Aequorea victoria (jellyfish)6100
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
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 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 2.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 148023 / Symmetry type: POINT
RefinementHighest resolution: 2.49 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0021960
ELECTRON MICROSCOPYf_angle_d0.4742666
ELECTRON MICROSCOPYf_dihedral_angle_d7.161279
ELECTRON MICROSCOPYf_chiral_restr0.037295
ELECTRON MICROSCOPYf_plane_restr0.004328

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