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Yorodumi- PDB-2d57: Double layered 2D crystal structure of AQUAPORIN-4 (AQP4M23) at 3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d57 | ||||||
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Title | Double layered 2D crystal structure of AQUAPORIN-4 (AQP4M23) at 3.2 a resolution by electron crystallography | ||||||
Components | Aquaporin-4 | ||||||
Keywords | TRANSPORT PROTEIN / WATER TRANSPORT / WATER CHANNEL / AQUAPORIN / TWO-DIMENSIONAL CRYSTAL / MEMBRANE PROTEIN / BACULOVIRUS EXPRESSION SYSTEM | ||||||
Function / homology | Function and homology information Passive transport by Aquaporins / cerebrospinal fluid secretion / renal water absorption / regulation of vascular endothelial growth factor production / cerebrospinal fluid circulation / astrocyte end-foot / intracellular water homeostasis / water transport / water channel activity / negative regulation of cell adhesion molecule production ...Passive transport by Aquaporins / cerebrospinal fluid secretion / renal water absorption / regulation of vascular endothelial growth factor production / cerebrospinal fluid circulation / astrocyte end-foot / intracellular water homeostasis / water transport / water channel activity / negative regulation of cell adhesion molecule production / cell projection membrane / multicellular organismal-level water homeostasis / Vasopressin regulates renal water homeostasis via Aquaporins / cellular response to interleukin-6 / negative regulation of interleukin-1 beta production / negative regulation of interleukin-6 production / cellular response to interleukin-1 / basal plasma membrane / response to glucocorticoid / T-tubule / cellular response to estradiol stimulus / establishment of localization in cell / female pregnancy / cellular response to glucose stimulus / sensory perception of sound / cell-cell adhesion / carbon dioxide transport / sarcolemma / cellular response to type II interferon / cell-cell junction / basolateral plasma membrane / protein homotetramerization / endosome membrane / external side of plasma membrane / protein-containing complex / extracellular region / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | ELECTRON CRYSTALLOGRAPHY / electron crystallography / MOLECULAR REPLACEMENT / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Hiroaki, Y. / Tani, K. / Kamegawa, A. / Gyobu, N. / Nishikawa, K. / Suzuki, H. / Walz, T. / Sasaki, S. / Mitsuoka, K. / Kimura, K. ...Hiroaki, Y. / Tani, K. / Kamegawa, A. / Gyobu, N. / Nishikawa, K. / Suzuki, H. / Walz, T. / Sasaki, S. / Mitsuoka, K. / Kimura, K. / Mizoguchi, A. / Fujiyoshi, Y. | ||||||
Citation | Journal: J Mol Biol / Year: 2006 Title: Implications of the aquaporin-4 structure on array formation and cell adhesion. Authors: Yoko Hiroaki / Kazutoshi Tani / Akiko Kamegawa / Nobuhiko Gyobu / Kouki Nishikawa / Hiroshi Suzuki / Thomas Walz / Sei Sasaki / Kaoru Mitsuoka / Kazushi Kimura / Akira Mizoguchi / Yoshinori Fujiyoshi / Abstract: Aquaporin-4 (AQP4) is the predominant water channel in the mammalian brain and an important drug target for treatment of cerebral edema, bipolar disorder and mesial temporal lobe epilepsy. We ...Aquaporin-4 (AQP4) is the predominant water channel in the mammalian brain and an important drug target for treatment of cerebral edema, bipolar disorder and mesial temporal lobe epilepsy. We determined the AQP4 structure by electron crystallography of double-layered, two-dimensional (2D) crystals. The structure allows us to discuss how the expression ratio between the long and short AQP4 splicing variant can determine the size of in vivo orthogonal arrays. Furthermore, AQP4 contains a short 3(10) helix in an extracellular loop, which mediates weak but specific interactions between AQP4 molecules in adjoining membranes. This finding suggests a previously unexpected role for AQP4 in cell adhesion. This notion was corroborated by expression of AQP4 in L-cells, which resulted in clustering of the cells. Our AQP4 structure thus enables us to propose models for the size regulation of orthogonal arrays and channel-mediated cell adhesion. | ||||||
History |
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Remark 240 | EXPERIMENT TYPE : ELECTRON DIFFRACTION DATE OF DATA COLLECTION : 01-APR-2002 TEMPERATURE (KELVIN) : ... EXPERIMENT TYPE : ELECTRON DIFFRACTION DATE OF DATA COLLECTION : 01-APR-2002 TEMPERATURE (KELVIN) : 4.2 PH : 6.00 NUMBER OF CRYSTALS USED : 135 RADIATION SOURCE : JEM3000SFF OPTICS : CRYSTALS TILTED TO MAX 60 DEGREES DETECTOR TYPE : CCD DETECTOR MANUFACTURER : GATAN ULTRASCAN INTENSITY INTEGRATION SOFTWARE : PICKYCOR, AN MRC ELECTRON DIFFRACTION PROGRAM DATA SCALING SOFTWARE : MERGEDIFF,AN MRC ELECTRON DIFFRACTION PROGRAM ACCELERATION VOLTAGE (KV) : 300 NUMBER OF UNIQUE REFLECTIONS : 5992 RESOLUTION RANGE HIGH (A) : 3.20 RESOLUTION RANGE LOW (A) : 22.21 OVERALL. COMPLETENESS FOR RANGE (%) : 87.0 DATA REDUNDANCY : NULL R MERGE (I) : 0.223 R SYM (I) : NULL FOR THE DATA SET : NULL IN THE HIGHEST RESOLUTION SHELL. HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.40 COMPLETENESS FOR SHELL (%) : 85.8 DATA REDUNDANCY IN SHELL : NULL R MERGE FOR SHELL (I) : 0.445 R SYM FOR SHELL (I) : NULL FOR SHELL : NULL METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT SOFTWARE USED: CNS STARTING MODEL: PDB ENTRY 1J4N |
-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 2d57.cif.gz | 54 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d57.ent.gz | 36.9 KB | Display | PDB format |
PDBx/mmJSON format | 2d57.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2d57_validation.pdf.gz | 422.4 KB | Display | wwPDB validaton report |
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Full document | 2d57_full_validation.pdf.gz | 441.7 KB | Display | |
Data in XML | 2d57_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 2d57_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/2d57 ftp://data.pdbj.org/pub/pdb/validation_reports/d5/2d57 | HTTPS FTP |
-Related structure data
Related structure data | 1j4nS 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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-Components
#1: Protein | Mass: 32189.381 Da / Num. of mol.: 1 / Fragment: residues 23-323 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Aqp4 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P47863 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON CRYSTALLOGRAPHY / Number of used crystals: 1 |
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EM experiment | Aggregation state: 2D ARRAY / 3D reconstruction method: electron crystallography |
-Sample preparation
Component | Name: AQUAPORIN 4 CRYSTAL / Type: COMPLEX |
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Specimen | Embedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
EM embedding | Details: 7% trehalose / Material: trehalose |
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.41 % |
Crystal grow | Temperature: 293 K / Method: dialysys / pH: 6 Details: 10mM MES(pH 6.0), 100mM NaCl, 50mM MgCl2, 2mM DTT, 1% glycerol, dialysys, temperature 293K |
-Data collection
Microscopy | Model: JEOL 3000SFF / Details: diffraction and images |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: DIFFRACTION |
Specimen holder | Cryogen: HELIUM |
Diffraction | Mean temperature: 4.2 K Ambient temp details: data was collected by electron microscope equipped with a helium stage |
Diffraction source | Source: ELECTRON MICROSCOPE / Wavelength: 0.01968 Å |
Detector | Type: GATAN ULTRASCAN / Detector: CCD / Date: Apr 1, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: electron |
Radiation wavelength | Wavelength: 0.01968 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→22.21 Å / Num. all: 6888 / Num. obs: 5992 / % possible obs: 87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.223 |
Reflection shell | Resolution: 3.2→3.4 Å / Rmerge(I) obs: 0.445 / % possible all: 85.8 |
-Processing
Software |
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3D reconstruction | Symmetry type: 2D CRYSTAL | ||||||||||||||||||||||||||||||||||||
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1J4N Resolution: 3.2→22.21 Å / Rfactor Rfree error: 0.018 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 83.0511 Å2 / ksol: 0.147131 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→22.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.4 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: protein_rep.param / Topol file: protein.top |