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- PDB-1ih5: CRYSTAL STRUCTURE OF AQUAPORIN-1 -

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Basic information

Entry
Database: PDB / ID: 1ih5
TitleCRYSTAL STRUCTURE OF AQUAPORIN-1
ComponentsAQUAPORIN-1
KeywordsMEMBRANE PROTEIN / WATER CHANNEL / TWO-DIMENSIONAL CRYSTAL
Function / homology
Function and homology information


metanephric descending thin limb development / metanephric proximal straight tubule development / metanephric proximal convoluted tubule segment 2 development / metanephric glomerulus vasculature development / hydrogen peroxide channel activity / nitric oxide transmembrane transporter activity / lipid digestion / cellular response to salt stress / renal water transport / corticotropin secretion ...metanephric descending thin limb development / metanephric proximal straight tubule development / metanephric proximal convoluted tubule segment 2 development / metanephric glomerulus vasculature development / hydrogen peroxide channel activity / nitric oxide transmembrane transporter activity / lipid digestion / cellular response to salt stress / renal water transport / corticotropin secretion / carbon dioxide transmembrane transport / renal water absorption / carbon dioxide transmembrane transporter activity / glycerol transmembrane transporter activity / secretory granule organization / water transmembrane transporter activity / Passive transport by Aquaporins / cerebrospinal fluid secretion / positive regulation of saliva secretion / pancreatic juice secretion / establishment or maintenance of actin cytoskeleton polarity / lateral ventricle development / glycerol transmembrane transport / cellular response to mercury ion / intracellularly cGMP-activated cation channel activity / potassium ion transmembrane transporter activity / intracellular water homeostasis / water transport / transepithelial water transport / water channel activity / ammonium transmembrane transport / ankyrin-1 complex / ammonium channel activity / glomerular filtration / camera-type eye morphogenesis / fibroblast migration / multicellular organismal-level water homeostasis / cellular homeostasis / cellular hyperosmotic response / cell volume homeostasis / hyperosmotic response / odontogenesis / positive regulation of fibroblast migration / : / nitric oxide transport / brush border / transmembrane transporter activity / cellular response to dexamethasone stimulus / potassium channel activity / renal water homeostasis / ephrin receptor binding / cellular response to retinoic acid / sensory perception of pain / cellular response to nitric oxide / basal plasma membrane / cellular response to copper ion / cellular response to cAMP / carbon dioxide transport / establishment of localization in cell / brush border membrane / wound healing / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / cellular response to mechanical stimulus / sarcolemma / potassium ion transport / cellular response to hydrogen peroxide / positive regulation of fibroblast proliferation / positive regulation of angiogenesis / apical part of cell / cellular response to UV / Vasopressin regulates renal water homeostasis via Aquaporins / nuclear membrane / defense response to Gram-negative bacterium / basolateral plasma membrane / cellular response to hypoxia / apical plasma membrane / axon / negative regulation of apoptotic process / extracellular exosome / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Aquaporin 1 / Glycerol uptake facilitator protein / Glycerol uptake facilitator protein. / Aquaporin transporter / Major intrinsic protein, conserved site / MIP family signature. / Major intrinsic protein / Major intrinsic protein / Aquaporin-like / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 3.7 Å
AuthorsRen, 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
DepositionApr 18, 2001Deposition site: RCSB / Processing site: RCSB
SupersessionApr 25, 2001ID: 1HW0
Revision 1.0Apr 25, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Author supporting evidence / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_image_scans / em_single_particle_entity
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: AQUAPORIN-1


Theoretical massNumber of molelcules
Total (without water)28,5501
Polymers28,5501
Non-polymers00
Water00
1
A: AQUAPORIN-1

A: AQUAPORIN-1

A: AQUAPORIN-1

A: AQUAPORIN-1


Theoretical massNumber of molelcules
Total (without water)114,2004
Polymers114,2004
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area10670 Å2
ΔGint-104 kcal/mol
Surface area41720 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)99.580, 99.580, 100.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein AQUAPORIN-1 / AQUAPORIN-CHIP / AQP-1


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

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: aquaporin / Type: COMPLEX
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Crystal grow
*PLUS
pH: 7.2 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.0 mg/mlprotein11
20.28-0.33 mg/mllipid11
370-120 mMdetergent11
420 mM11NaH2PO4/Na2HPO4
5100 mM11NaCl
60.1 mMEDTA11
70.025 %(w/v)11NaN3

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Data collection

MicroscopyModel: FEI/PHILIPS CM200FEG
Electron gunElectron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION
DetectorDate: Jan 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: electron
Radiation wavelengthRelative weight: 1
ReflectionBiso Wilson estimate: 38.1 Å2
Reflection
*PLUS
Highest resolution: 3.7 Å / Num. obs: 19839 / % possible obs: 63 % / Num. measured all: 48037

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Processing

SoftwareName: X-PLOR / Classification: refinement
3D reconstructionResolution: 3.7 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES
RefinementResolution: 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
RfactorNum. reflection% reflectionSelection details
Rfree0.458 309 -RANDOM
Rwork0.361 ---
obs0.361 4433 77.1 %-
Displacement parametersBiso mean: 47.8 Å2
Refinement stepCycle: LAST / Resolution: 3.7→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1645 0 0 0 1645

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