+Open data
-Basic information
Entry | Database: PDB / ID: 1ih5 | |||||||||
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Title | CRYSTAL STRUCTURE OF AQUAPORIN-1 | |||||||||
Components | AQUAPORIN-1 | |||||||||
Keywords | MEMBRANE PROTEIN / WATER CHANNEL / TWO-DIMENSIONAL CRYSTAL | |||||||||
Function / homology | Function and homology information nitric oxide transmembrane transporter activity / metanephric descending thin limb development / metanephric proximal straight tubule development / metanephric proximal convoluted tubule segment 2 development / metanephric glomerulus vasculature development / cerebrospinal fluid secretion / lipid digestion / cellular response to salt stress / renal water transport / glycerol transmembrane transporter activity ...nitric oxide transmembrane transporter activity / metanephric descending thin limb development / metanephric proximal straight tubule development / metanephric proximal convoluted tubule segment 2 development / metanephric glomerulus vasculature development / cerebrospinal fluid secretion / lipid digestion / cellular response to salt stress / renal water transport / glycerol transmembrane transporter activity / corticotropin secretion / secretory granule organization / carbon dioxide transmembrane transport / carbon dioxide transmembrane transporter activity / renal water absorption / positive regulation of saliva secretion / Passive transport by Aquaporins / glycerol transmembrane transport / water transmembrane transporter activity / establishment or maintenance of actin cytoskeleton polarity / pancreatic juice secretion / cellular response to mercury ion / lateral ventricle development / potassium ion transmembrane transporter activity / : / intracellular water homeostasis / water transport / water channel activity / transepithelial water transport / glomerular filtration / ammonium transmembrane transport / ankyrin-1 complex / intracellularly cGMP-activated cation channel activity / ammonium channel activity / camera-type eye morphogenesis / fibroblast migration / multicellular organismal-level water homeostasis / cellular homeostasis / hyperosmotic response / cellular hyperosmotic response / renal water homeostasis / cell volume homeostasis / positive regulation of fibroblast migration / odontogenesis / cellular response to nitric oxide / nitric oxide transport / cGMP-mediated signaling / brush border / transmembrane transporter activity / potassium channel activity / cellular response to dexamethasone stimulus / basal plasma membrane / cellular response to retinoic acid / cellular response to cAMP / sensory perception of pain / cellular response to copper ion / ephrin receptor binding / potassium ion transport / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / establishment of localization in cell / brush border membrane / wound healing / carbon dioxide transport / cellular response to mechanical stimulus / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / sarcolemma / Vasopressin regulates renal water homeostasis via Aquaporins / positive regulation of fibroblast proliferation / cellular response to hydrogen peroxide / positive regulation of angiogenesis / cellular response to UV / apical part of cell / cellular response to hypoxia / basolateral plasma membrane / nuclear membrane / defense response to Gram-negative bacterium / apical plasma membrane / axon / negative regulation of apoptotic process / extracellular exosome / identical protein binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Ren, G. / Reddy, V.S. / Cheng, A. / Melnyk, P. / Mitra, A.K. | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2001 Title: Visualization of a water-selective pore by electron crystallography in vitreous ice. Authors: G Ren / V S Reddy / A Cheng / P Melnyk / A K Mitra / Abstract: The water-selective pathway through the aquaporin-1 membrane channel has been visualized by fitting an atomic model to a 3.7-A resolution three-dimensional density map. This map was determined by ...The water-selective pathway through the aquaporin-1 membrane channel has been visualized by fitting an atomic model to a 3.7-A resolution three-dimensional density map. This map was determined by analyzing images and electron diffraction patterns of lipid-reconstituted two-dimensional crystals of aquaporin-1 preserved in vitrified buffer in the absence of any additive. The aqueous pathway is characterized by a size-selective pore that is approximately 4.0 +/- 0.5A in diameter, spans a length of approximately 18A, and bends by approximately 25 degrees as it traverses the bilayer. This narrow pore is connected by wide, funnel-shaped openings at the extracellular and cytoplasmic faces. The size-selective pore is outlined mostly by hydrophobic residues, resulting in a relatively inert pathway conducive to diffusion-limited water flow. The apex of the curved pore is close to the locations of the in-plane pseudo-2-fold symmetry axis that relates the N- and C-terminal halves and the conserved, functionally important N76 and N192 residues. #1: Journal: J.Mol.Biol. / Year: 2000 Title: Three-Dimensional Fold of the Human Aqp1 Water Channel Determined at 4 A Resolution by Electron Crystallography of Two-Dimensional Crystals Embedded in Ice Authors: Ren, G. / Cheng, A. / Reddy, V. / Melnyk, P. / Mitra, A.K. #2: Journal: J.Struct.Biol. / Year: 2000 Title: Polymorphism in the Packing of Aquaporin-1 Tetramers in 2-D Crystals Authors: Ren, G. / Cheng, A. / Melnyk, P. / Mitra, A.K. #3: Journal: Nature / Year: 1997 Title: Three-Dimensional Organization of a Human Water Channel Authors: Cheng, A. / Van Hoek, A.N. / Yeager, M. / Verkman, A.S. / Mitra, A.K. | |||||||||
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 | 1ih5.cif.gz | 48.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ih5.ent.gz | 34.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ih5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ih5_validation.pdf.gz | 359.6 KB | Display | wwPDB validaton report |
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Full document | 1ih5_full_validation.pdf.gz | 381.5 KB | Display | |
Data in XML | 1ih5_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 1ih5_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/1ih5 ftp://data.pdbj.org/pub/pdb/validation_reports/ih/1ih5 | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 28549.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: RED-BLOOD CELL / Cellular location: MEMBRANE / References: UniProt: P29972 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON CRYSTALLOGRAPHY |
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EM experiment | Aggregation state: 2D ARRAY / 3D reconstruction method: electron crystallography |
-Sample preparation
Component | Name: aquaporin / Type: COMPLEX | ||||||||||||||||||||||||||||||||||||||||||||||||
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.2 / Method: unknown | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Microscopy | Model: FEI/PHILIPS CM200FEG |
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Electron gun | Electron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM |
Electron lens | Mode: DIFFRACTION |
Detector | Date: Jan 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: electron |
Radiation wavelength | Relative weight: 1 |
Reflection | Biso Wilson estimate: 38.1 Å2 |
Reflection | *PLUS Highest resolution: 3.7 Å / Num. obs: 19839 / % possible obs: 63 % / Num. measured all: 48037 |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||
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3D reconstruction | Resolution: 3.7 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES | ||||||||||||||||||||
Refinement | Resolution: 3.7→24 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 2 Details: POSITIONAL REFINEMENT USING X-PLOR. REFINEMENT MONITORED BY RFREE AND PHIFREE (<| CALCLD. PHASE - EXPTL. OBSERVED PHASE|>). PSEUDO 2-FOLD SYMMETRY IN THE PLANE OF THE BILAYER RELATES THE N- AND C-TERMINAL HALVES
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Displacement parameters | Biso mean: 47.8 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.7→24 Å
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