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- PDB-8sjy: Structure of lens aquaporin-0 array in sphingomyelin/cholesterol ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8sjy | ||||||
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Title | Structure of lens aquaporin-0 array in sphingomyelin/cholesterol bilayer (1SM:2Chol) | ||||||
![]() | Lens fiber major intrinsic protein | ||||||
![]() | MEMBRANE PROTEIN / aquaporin / lens / cholesterol / lipid raft | ||||||
Function / homology | ![]() gap junction-mediated intercellular transport / water transport / water channel activity / structural constituent of eye lens / gap junction / response to stimulus / lens development in camera-type eye / positive regulation of cell adhesion / visual perception / protein homotetramerization ...gap junction-mediated intercellular transport / water transport / water channel activity / structural constituent of eye lens / gap junction / response to stimulus / lens development in camera-type eye / positive regulation of cell adhesion / visual perception / protein homotetramerization / calmodulin binding / apical plasma membrane / endoplasmic reticulum / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON CRYSTALLOGRAPHY / electron crystallography / ![]() | ||||||
![]() | Chiu, P.-L. / Walz, T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of aquaporin-0 arrays in sphingomyelin/cholesterol membranes and implications for lipid rafts Authors: Chiu, P.-L. / Walz, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.2 KB | Display | ![]() |
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PDB format | ![]() | 47.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 823.8 KB | Display | ![]() |
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Full document | ![]() | 929.4 KB | Display | |
Data in XML | ![]() | 13.6 KB | Display | |
Data in CIF | ![]() | 16.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28284.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||
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#2: Chemical | ChemComp-HWP / [( #3: Chemical | ChemComp-CLR / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON CRYSTALLOGRAPHY | |||
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EM experiment | Aggregation state: 2D ARRAY / 3D reconstruction method: electron crystallography | |||
Crystal symmetry | Image processing-ID: 1 / ∠γ: 90 ° / C sampling length: 200 Å / A: 65.5 Å / B: 65.5 Å / C: 200 Å / Space group name H-M: P422
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Sample preparation
Component | Name: Lens aquaporin-0 in sphingomyelin/cholesterol bilayer / Type: COMPLEX / Entity ID: #1 / Source: NATURAL | |||||||||||||||||||||||||
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Molecular weight | Value: 0.0283 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: ![]() ![]() | |||||||||||||||||||||||||
EM crystal formation | Lipid mixture: Sphingomyelin and cholesterol were mixed at a 1:2 molar ratio. Lipid protein ratio: 0.2 / Temperature: 310 K / Time: 7 DAY | |||||||||||||||||||||||||
Buffer solution | pH: 6 Details: 10 mM MES (pH 6.0), 300 mM NaCl, 30 mM MgCl2, and 0.05% NaN3 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO / Details: 2D crystal of lens AQP0. | |||||||||||||||||||||||||
Specimen support | Grid material: MOLYBDENUM / Grid type: Homemade | |||||||||||||||||||||||||
EM embedding | Details: Aquaporin-0 2D crystals were prepared on molybdenum grids using the carbon sandwich method and a trehalose concentration ranging from 3% to 5% (w/v). Material: Trehalose |
-Data collection
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 Details: The diffraction patterns were recorded without setting defocus. |
Electron gun | Electron source: ![]() |
Electron lens | Mode: DIFFRACTION / Nominal defocus max: 0 nm / Nominal defocus min: 0 nm / Calibrated defocus min: 0 nm / Calibrated defocus max: 0 nm / C2 aperture diameter: 30 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: OTHER |
Image recording | Average exposure time: 30 sec. / Electron dose: 10 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Num. of diffraction images: 241 |
EM diffraction shell | Resolution: 2.3→11.8 Å / Fourier space coverage: 90.19 % / Multiplicity: 6.3 / Num. of structure factors: 17031 / Phase residual: 1.0E-6 ° |
EM diffraction stats | Details: There was no phase error rejection criteria used for diffraction intensities. Fourier space coverage: 90.19 % / High resolution: 2.3 Å / Num. of intensities measured: 127703 / Num. of structure factors: 17031 / Phase error rejection criteria: 0 / Rmerge: 19.9 / Rsym: 13.8 |
Reflection | Biso Wilson estimate: 31.17 Å2 |
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Processing
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EM software |
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Crystal symmetry | Image processing-ID: 1 / ∠γ: 90 ° / C sampling length: 200 Å / A: 65.5 Å / B: 65.5 Å / C: 200 Å / Space group name H-M: P422
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CTF correction | Type: NONE | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.5 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 2D CRYSTAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 2B6O Pdb chain-ID: A / Accession code: 2B6O / Chain residue range: 6-255 / Details: Molecular replacement / Pdb chain residue range: 6-255 / Source name: PDB / Type: experimental model | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.15 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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LS refinement shell |
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