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- EMDB-15528: AQP7 dimer of tetramers_D4 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-15528
TitleAQP7 dimer of tetramers_D4
Map data
Sample
  • Complex: dimer of tetramers
    • Protein or peptide: Aquaporin-7
  • Ligand: water
Keywordsmembrane channel / octamer / adhesion protein / junction protein / MEMBRANE PROTEIN
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 / cell-cell junction ...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 / cell-cell junction / 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)
Methodsingle 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, 2 items
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, 2022-
Header (metadata) releaseFeb 15, 2023-
Map releaseFeb 15, 2023-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15528.png

Downloads & links

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Map

FileDownload / File: emd_15528.map.gz / Format: CCP4 / Size: 244.1 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 400 pix.
= 338.56 Å		0.85 Å/pix.
x 400 pix.
= 338.56 Å		0.85 Å/pix.
x 400 pix.
= 338.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8464 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.2014983 - 1.6308234
Average (Standard dev.)0.00096460216 (±0.045448393)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 338.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_15528_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_15528_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : dimer of tetramers

EntireName: dimer of tetramers
Components
  • Complex: dimer of tetramers
    • Protein or peptide: Aquaporin-7
  • Ligand: water

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Supramolecule #1: dimer of tetramers

SupramoleculeName: dimer of tetramers / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Aquaporin-7

MacromoleculeName: Aquaporin-7 / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.264395 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MVQASGHRRS TRGSKMVSWS VIAKIQEILQ RKMVREFLAE FMSTYVMMVF GLGSVAHMVL NKKYGSYLGV NLGFGFGVTM GVHVAGRIS GAHMNAAVTF ANCALGRVPW RKFPVYVLGQ FLGSFLAAAT IYSLFYTAIL HFSGGQLMVT GPVATAGIFA T YLPDHMTL ...String:
MVQASGHRRS TRGSKMVSWS VIAKIQEILQ RKMVREFLAE FMSTYVMMVF GLGSVAHMVL NKKYGSYLGV NLGFGFGVTM GVHVAGRIS GAHMNAAVTF ANCALGRVPW RKFPVYVLGQ FLGSFLAAAT IYSLFYTAIL HFSGGQLMVT GPVATAGIFA T YLPDHMTL WRGFLNEAWL TGMLQLCLFA ITDQENNPAL PGTEALVIGI LVVIIGVSLG MNTGYAINPS RDLPPRIFTF IA GWGKQVF SNGENWWWVP VVAPLLGAYL GGIIYLVFIG STIPREPLKL EDSVAYEDHG ITVLPKMGSH EPTISPLTPV SVS PANRSS VHPAPPLHES MALEHF

UniProtKB: Aquaporin-7

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 57 / 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

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMNa3PO4sodium phosphate
100.0 mMNaClsodium chloride
0.01 %C56H92O2GDN
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Details: 20mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK II / Details: 3s blot, 3s wait, 0s drain time, 0 blot force.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 14000 / Average exposure time: 2.0 sec. / Average electron dose: 50.0 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: 2.2 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 371567
Details: Those particles were picked from the sub-dataset of 3225 micrographs by template picking tool.
Startup modelType of model: OTHER
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D4 (2x4 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 102367
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 5 / Software - Name: cryoSPARC

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 98.6
Output model

PDB-8amx:
AQP7 dimer of tetramers_D4

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