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- PDB-1fqy: STRUCTURE OF AQUAPORIN-1 AT 3.8 A RESOLUTION BY ELECTRON CRYSTALL... -

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Entry
Database: PDB / ID: 1fqy
TitleSTRUCTURE OF AQUAPORIN-1 AT 3.8 A RESOLUTION BY ELECTRON CRYSTALLOGRAPHY
ComponentsAQUAPORIN-1
KeywordsMEMBRANE 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 / lateral ventricle development / cellular response to mercury ion / potassium ion transmembrane transporter activity / water channel activity / intracellular water homeostasis / cellular response to inorganic substance / intracellularly cGMP-activated cation channel activity / ammonium transmembrane transport / water transport / transepithelial water transport / glomerular filtration / ankyrin-1 complex / ammonium transmembrane transporter activity / camera-type eye morphogenesis / multicellular organismal-level water homeostasis / fibroblast migration / cellular homeostasis / cellular hyperosmotic response / hyperosmotic response / renal water homeostasis / cell volume homeostasis / positive regulation of fibroblast migration / odontogenesis / nitric oxide transport / cGMP-mediated signaling / brush border / potassium channel activity / transmembrane transporter activity / cellular response to nitric oxide / cellular response to retinoic acid / cellular response to cAMP / sensory perception of pain / cellular response to copper ion / ephrin receptor binding / cellular response to dexamethasone stimulus / basal plasma membrane / establishment of localization in cell / brush border membrane / sarcolemma / carbon dioxide transport / wound healing / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / potassium ion transport / cellular response to hydrogen peroxide / Vasopressin regulates renal water homeostasis via Aquaporins / cellular response to mechanical stimulus / positive regulation of angiogenesis / cellular response to UV / positive regulation of fibroblast proliferation / 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
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: 3.8 Å
AuthorsMurata, K. / Mitsuoka, K. / Hirai, T. / Walz, T. / Agre, P. / Heymann, J.B. / Engel, A. / Fujiyoshi, Y.
CitationJournal: Nature / Year: 2000
Title: Structural determinants of water permeation through aquaporin-1.
Authors: K Murata / K Mitsuoka / T Hirai / T Walz / P Agre / J B Heymann / A Engel / Y Fujiyoshi /
Abstract: Human red cell AQP1 is the first functionally defined member of the aquaporin family of membrane water channels. Here we describe an atomic model of AQP1 at 3.8A resolution from electron ...Human red cell AQP1 is the first functionally defined member of the aquaporin family of membrane water channels. Here we describe an atomic model of AQP1 at 3.8A resolution from electron crystallographic data. Multiple highly conserved amino-acid residues stabilize the novel fold of AQP1. The aqueous pathway is lined with conserved hydrophobic residues that permit rapid water transport, whereas the water selectivity is due to a constriction of the pore diameter to about 3 A over a span of one residue. The atomic model provides a possible molecular explanation to a longstanding puzzle in physiology-how membranes can be freely permeable to water but impermeable to protons.
History
DepositionSep 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 17, 2024Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_sf

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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
Water0
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 area12140 Å2
ΔGint-96 kcal/mol
Surface area38710 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)96.000, 96.000, 100.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
DetailsThe biological assembly is a tetramer constructed from chain A

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Components

#1: Protein AQUAPORIN-1 / / AQP1


Mass: 28549.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: ERYTHROCYTE / References: UniProt: P29972

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY / Number of used crystals: 135
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: aquaporin / Type: COMPLEX
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: MOLYBDENUM
EM embeddingDetails: 3% / Material: trehalose
Crystal growTemperature: 298 K / Method: dialysis with continuous flow dialysis machine / pH: 6
Details: Escherichia coli lipids, magnesium chloride, sodium chloride, MES, pH 6.0, Dialysis with continuous flow dialysis machine, temperature 298K
Crystal grow
*PLUS
Details: Eletron Diffraction

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Data collection

MicroscopyModel: JEOL 3000SFF / Details: diffraction patterns and images collected
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION
Specimen holderCryogen: HELIUM
Image recordingElectron dose: 20 e/Å2 / Film or detector model: GENERIC FILM / Details: digitized using LeafScan45 scanner (Scitex)
Image scansScanner model: OTHER
DiffractionMean temperature: 4 K
Diffraction sourceSource: ELECTRON MICROSCOPE / Type: JEOL 3000 SFF / Wavelength: 0.0197
DetectorType: GATAN Model 795 MegaScan / Detector: CCD / Date: Jun 7, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: electron
Radiation wavelengthWavelength: 0.0197 Å / Relative weight: 1
ReflectionResolution: 3.8→96 Å / Num. all: 85254 / Num. obs: 85254 / % possible obs: 88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.8 % / Biso Wilson estimate: 8.14 Å2 / Rmerge(I) obs: 0.495 / Net I/σ(I): 1.1
Reflection shellResolution: 3.8→3.9 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.703 / Num. unique all: 4010 / % possible all: 86.9

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Processing

Software
NameVersionClassification
LATLINEmodel building
X-PLOR3.851refinement
CCP4(TRUNCATE)data scaling
LATLINEphasing
3D reconstructionResolution: 3.8 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES
RefinementResolution: 3.8→6 Å / σ(F): 1 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: For refinement with phase restraint, we used the structure factors merged from both electron diffraction patterns and images. Thus in this file we included the structure factors with phases ...Details: For refinement with phase restraint, we used the structure factors merged from both electron diffraction patterns and images. Thus in this file we included the structure factors with phases used in the refinement. The observed phases were labelled as calculated phases here.
RfactorNum. reflection% reflectionSelection details
Rfree0.417 124 0.036 %RANDOM
Rwork0.399 ---
all0.406 1846 --
obs0.406 1846 50.8 %-
Refine analyzeLuzzati coordinate error obs: 0.85 Å
Refinement stepCycle: LAST / Resolution: 3.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1661 0 0 0 1661
Refine LS restraints
Refine-IDTypeDev ideal
ELECTRON CRYSTALLOGRAPHYx_bond_d0.017
ELECTRON CRYSTALLOGRAPHYx_angle_deg2.794
LS refinement shellResolution: 3.8→3.93 Å / Total num. of bins used: 8
Rfactor% reflection
Rfree0.31 1.58 %
Rwork0.424 -
obs-36.3 %

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