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- PDB-8amx: AQP7 dimer of tetramers_D4 -

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Basic information

Entry
Database: PDB / ID: 8amx
TitleAQP7 dimer of tetramers_D4
ComponentsAquaporin-7
KeywordsMEMBRANE PROTEIN / membrane channel / octamer / adhesion protein / junction protein
Function / homology
Function and homology information


Transport of glycerol from adipocytes to the liver by Aquaporins / glycerol channel activity / urea transmembrane transporter activity / Passive transport by Aquaporins / glycerol transmembrane transport / water channel activity / water transport / lipid droplet / cytoplasmic vesicle membrane / cell-cell junction ...Transport of glycerol from adipocytes to the liver by Aquaporins / glycerol channel activity / urea transmembrane transporter activity / Passive transport by Aquaporins / glycerol transmembrane transport / water channel activity / water transport / lipid droplet / cytoplasmic vesicle membrane / cell-cell junction / cell cortex / basolateral plasma membrane / plasma membrane / cytoplasm
Similarity search - Function
: / Major intrinsic protein / Major intrinsic protein / Aquaporin-like
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsHuang, P. / Venskutonyte, R. / Fan, X. / Li, P. / Yan, N. / Gourdon, P. / Lindkvist-Petersson, K.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council2017-05816, 2016-01319 Sweden
Other governmentSwedish Cancer Society 20 0747 PjF
CitationJournal: Nat Commun / Year: 2023
Title: Cryo-EM structure supports a role of AQP7 as a junction protein.
Authors: Peng Huang / Raminta Venskutonytė / Rashmi B Prasad / Hamidreza Ardalani / Sofia W de Maré / Xiao Fan / Ping Li / Peter Spégel / Nieng Yan / Pontus Gourdon / Isabella Artner / Karin Lindkvist-Petersson /
Abstract: Aquaglyceroporin 7 (AQP7) facilitates glycerol flux across the plasma membrane with a critical physiological role linked to metabolism, obesity, and associated diseases. Here, we present the single- ...Aquaglyceroporin 7 (AQP7) facilitates glycerol flux across the plasma membrane with a critical physiological role linked to metabolism, obesity, and associated diseases. Here, we present the single-particle cryo-EM structure of AQP7 determined at 2.55 Å resolution adopting two adhering tetramers, stabilized by extracellularly exposed loops, in a configuration like that of the well-characterized interaction of AQP0 tetramers. The central pore, in-between the four monomers, displays well-defined densities restricted by two leucine filters. Gas chromatography mass spectrometry (GC/MS) results show that the AQP7 sample contains glycerol 3-phosphate (Gro3P), which is compatible with the identified features in the central pore. AQP7 is shown to be highly expressed in human pancreatic α- and β- cells suggesting that the identified AQP7 octamer assembly, in addition to its function as glycerol channel, may serve as junction proteins within the endocrine pancreas.
History
DepositionAug 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _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-7
B: Aquaporin-7
C: Aquaporin-7
D: Aquaporin-7
E: Aquaporin-7
F: Aquaporin-7
G: Aquaporin-7
H: Aquaporin-7


Theoretical massNumber of molelcules
Total (without water)298,1158
Polymers298,1158
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area31230 Å2
ΔGint-298 kcal/mol
Surface area70240 Å2
MethodPISA

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Components

#1: Protein
Aquaporin-7 / AQP-7 / Aquaglyceroporin-7 / Aquaporin adipose / AQPap / Aquaporin-7-like


Mass: 37264.395 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AQP7, AQP7L, AQP9 / Production host: Komagataella pastoris (fungus) / References: UniProt: O14520
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

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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: dimer of tetramers / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Komagataella pastoris (fungus)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMsodium phosphateNa3PO41
2100 mMsodium chlorideNaCl1
30.01 %GDNC56H92O21
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 20mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: 3s blot, 3s wait, 0s drain time, 0 blot force

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN 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: 2200 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 2 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 14000

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 371567
Details: Those particles were picked from the sub-dataset of 3225 micrographs by template picking tool.
SymmetryPoint symmetry: D4 (2x4 fold dihedral)
3D reconstructionResolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 102367 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 98.6 / Protocol: RIGID BODY FIT / Space: REAL

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