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Yorodumi- PDB-3m9i: Electron crystallographic structure of lens Aquaporin-0 (AQP0) (l... -
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-Basic information
Entry | Database: PDB / ID: 3m9i | ||||||
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Title | Electron crystallographic structure of lens Aquaporin-0 (AQP0) (lens MIP) in E. coli polar lipids | ||||||
Components | Lens fiber major intrinsic protein | ||||||
Keywords | MEMBRANE PROTEIN / water channel / lens / lipid-protein interactions | ||||||
Function / homology | Function and homology information gap junction-mediated intercellular transport / water transport / water channel activity / structural constituent of eye lens / gap junction / lens development in camera-type eye / positive regulation of cell adhesion / visual perception / protein homotetramerization / calmodulin binding ...gap junction-mediated intercellular transport / water transport / water channel activity / structural constituent of eye lens / gap junction / 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 | Ovis aries (sheep) | ||||||
Method | ELECTRON CRYSTALLOGRAPHY / electron crystallography / MOLECULAR REPLACEMENT / cryo EM / Resolution: 2.5 Å | ||||||
Authors | Hite, R.K. / Li, Z. / Walz, T. | ||||||
Citation | Journal: EMBO J / Year: 2010 Title: Principles of membrane protein interactions with annular lipids deduced from aquaporin-0 2D crystals. Authors: Richard K Hite / Zongli Li / Thomas Walz / Abstract: We have previously described the interactions of aquaporin-0 (AQP0) with dimyristoyl phosphatidylcholine (DMPC) lipids. We have now determined the 2.5 A structure of AQP0 in two-dimensional (2D) ...We have previously described the interactions of aquaporin-0 (AQP0) with dimyristoyl phosphatidylcholine (DMPC) lipids. We have now determined the 2.5 A structure of AQP0 in two-dimensional (2D) crystals formed with Escherichia coli polar lipids (EPLs), which differ from DMPC both in headgroups and acyl chains. Comparison of the two structures shows that AQP0 does not adapt to the different length of the acyl chains in EPLs and that the distance between the phosphodiester groups in the two leaflets of the DMPC and EPL bilayers is almost identical. The EPL headgroups interact differently with AQP0 than do those of DMPC, but the acyl chains in the EPL and DMPC bilayers occupy similar positions. The interactions of annular lipids with membrane proteins seem to be driven by the propensity of the acyl chains to fill gaps in the protein surface. Interactions of the lipid headgroups may be responsible for the specific interactions found in tightly bound lipids but seem to have a negligible effect on interactions of generic annular lipids with membrane proteins. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3m9i.cif.gz | 63.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3m9i.ent.gz | 45.9 KB | Display | PDB format |
PDBx/mmJSON format | 3m9i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3m9i_validation.pdf.gz | 672.1 KB | Display | wwPDB validaton report |
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Full document | 3m9i_full_validation.pdf.gz | 695.9 KB | Display | |
Data in XML | 3m9i_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 3m9i_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m9/3m9i ftp://data.pdbj.org/pub/pdb/validation_reports/m9/3m9i | HTTPS FTP |
-Related structure data
Related structure data | 2b6oS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The octamer can be generated by applying P422 symmetry. |
-Components
#1: Protein | Mass: 23514.447 Da / Num. of mol.: 1 / Fragment: UNP residues 7 to 226 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: Q6J8I9 | ||
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#2: Chemical | ChemComp-3PE / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON CRYSTALLOGRAPHY / Number of used crystals: 281 |
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EM experiment | Aggregation state: 2D ARRAY / 3D reconstruction method: electron crystallography |
-Sample preparation
Component | Name: lens Aquaporin 0 / Type: COMPLEX |
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Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Purified membranes were solubilized in 4% (w/v) octyl glucoside in 10 mM Tris (pH 8.0) for 30 min at 22C |
Crystal grow | Temperature: 300 K / Method: microdialysis / pH: 6 Details: 100 mM NaCl, 50mM MgCl2, 10mM MES pH 6.0, MICRODIALYSIS, temperature 300K |
-Data collection
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: DIFFRACTION |
Image recording | Film or detector model: GENERIC GATAN (4k x 4k) |
Diffraction | Mean temperature: 279 K |
Diffraction source | Source: ELECTRON MICROSCOPE / Type: OTHER |
Detector | Type: Gatan / Detector: CCD / Date: Feb 24, 2009 |
Reflection | Resolution: 2.5→15.89 Å / Num. all: 14417 / Num. obs: 14417 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.226 / Rsym value: 0.189 |
Reflection shell | Resolution: 2.5→2.66 Å / Redundancy: 4 % / Num. unique all: 1935 / % possible all: 83.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2B6O Resolution: 2.5→15.89 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2341911.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.0682 Å2 / ksol: 0.1 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→15.89 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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