+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15528 | |||||||||
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Title | AQP7 dimer of tetramers_D4 | |||||||||
Map data | ||||||||||
Sample |
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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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.55 Å | |||||||||
Authors | Huang P / Venskutonyte R / Fan X / Li P / Yan N / Gourdon P / Lindkvist-Petersson K | |||||||||
Funding support | Sweden, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15528.map.gz | 125.9 MB | EMDB map data format | |
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Header (meta data) | emd-15528-v30.xml emd-15528.xml | 17.6 KB 17.6 KB | Display Display | EMDB header |
Images | emd_15528.png | 38 KB | ||
Others | emd_15528_half_map_1.map.gz emd_15528_half_map_2.map.gz | 225.9 MB 225.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15528 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15528 | HTTPS FTP |
-Related structure data
Related structure data | 8amxMC 8amwC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_15528.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8464 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_15528_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_15528_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : dimer of tetramers
Entire | Name: dimer of tetramers |
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Components |
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-Supramolecule #1: dimer of tetramers
Supramolecule | Name: dimer of tetramers / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Aquaporin-7
Macromolecule | Name: Aquaporin-7 / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 37.264395 KDa |
Recombinant expression | Organism: Komagataella pastoris (fungus) |
Sequence | String: 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 |
-Macromolecule #2: water
Macromolecule | Name: water / type: ligand / ID: 2 / Number of copies: 57 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: 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 | ||||||||||||
Vitrification | Cryogen 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. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film 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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 371567 Details: Those particles were picked from the sub-dataset of 3225 micrographs by template picking tool. |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final 3D classification | Number classes: 5 / Software - Name: cryoSPARC |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Number 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 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 98.6 |
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Output model | PDB-8amx: |