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- PDB-1j4n: Crystal Structure of the AQP1 water channel -

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Basic information

Entry
Database: PDB / ID: 1j4n
TitleCrystal Structure of the AQP1 water channel
ComponentsAQUAPORIN 1Aquaporin-1
KeywordsMEMBRANE PROTEIN / CHANNEL PROTEIN / TRANSMEMBRANE HELICES
Function / homology
Function and homology information


: / dense core granule membrane / Passive transport by Aquaporins / ammonium transmembrane transport => GO:0072488 / 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 / Erythrocytes take up carbon dioxide and release oxygen ...: / dense core granule membrane / Passive transport by Aquaporins / ammonium transmembrane transport => GO:0072488 / 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 / Erythrocytes take up carbon dioxide and release oxygen / Erythrocytes take up oxygen and release carbon dioxide / 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 / symbiont-containing vacuole / renal water absorption / positive regulation of saliva secretion / glycerol transmembrane transport / water transmembrane transporter activity / establishment or maintenance of actin cytoskeleton polarity / lateral ventricle development / cellular response to mercury ion / water channel activity / intracellular water homeostasis / cellular response to inorganic substance / intracellularly cGMP-activated cation channel activity / water transport / transepithelial water transport / glomerular filtration / response to xenobiotic stimulus => GO:0009410 / ammonium transmembrane transporter activity / camera-type eye morphogenesis / cellular homeostasis / cellular hyperosmotic response / hyperosmotic response / cell volume homeostasis / nitric oxide transport / Vasopressin regulates renal water homeostasis via Aquaporins / cGMP-mediated signaling / brush border / potassium channel activity / transmembrane transporter activity / 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 / caveola / brush border membrane / sarcolemma / carbon dioxide transport / wound healing / cellular response to hydrogen peroxide / 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 / membrane => GO:0016020 / positive regulation of cell migration / apical plasma membrane / axon / negative regulation of apoptotic process / extracellular exosome / nucleus / plasma membrane
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 speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsSui, H. / Han, B.-G. / Lee, J.K. / Walian, P. / Jap, B.K.
CitationJournal: Nature / Year: 2001
Title: Structural basis of water-specific transport through the AQP1 water channel.
Authors: Sui, H. / Han, B.G. / Lee, J.K. / Walian, P. / Jap, B.K.
History
DepositionOct 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AQUAPORIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7444
Polymers28,8241
Non-polymers9193
Water2,054114
1
A: AQUAPORIN 1
hetero molecules

A: AQUAPORIN 1
hetero molecules

A: AQUAPORIN 1
hetero molecules

A: AQUAPORIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,97416
Polymers115,2984
Non-polymers3,67712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area16090 Å2
ΔGint-115 kcal/mol
Surface area40130 Å2
MethodPISA, PQS
2
A: AQUAPORIN 1
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)237,94832
Polymers230,5958
Non-polymers7,35324
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_655-x+1,y,-z1
crystal symmetry operation6_565x,-y+1,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area35890 Å2
ΔGint-247 kcal/mol
Surface area76550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.331, 93.331, 180.49
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number97
Space group name H-MI422

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Components

#1: Protein AQUAPORIN 1 / Aquaporin-1 / AQP1 / Aquaporin-CHIP / Water channel protein for red blood cells and kidney proximal tubule


Mass: 28824.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: blood / References: UniProt: P47865
#2: Sugar ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.41 Å3/Da / Density % sol: 63.91 %
Description: Data collected at ALS was used for final data processing. Data collected at NSLS was used for initial data processing.
Crystal growTemperature: 277 K / Method: evaporation / pH: 7.5
Details: PEG, monomethyl ether 550, Tris-HCl, NG, pH 7.5, EVAPORATION, temperature 277K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / Details: Sui, H., (2000) Acta Crystallogr., D56, 1198.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
220 mMTris-HCl1droppH7.5
320 %PEG550 MME1reservoir
410 mMTris-HCl1reservoirpH7.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONALS 5.0.211.0367
SYNCHROTRONNSLS X252
DetectorType: ADSC / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0367 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. all: 20605 / Num. obs: 19626 / % possible obs: 95.2 % / Observed criterion σ(I): 0 / Redundancy: 15.8 % / Biso Wilson estimate: 42.7 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 41.8
Reflection shellResolution: 2.2→2.34 Å / Rmerge(I) obs: 0.58 / Num. unique all: 2450 / % possible all: 94.6
Reflection
*PLUS
% possible obs: 99.7 % / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
Lowest resolution: 2.3 Å / % possible obs: 100 % / Rmerge(I) obs: 0.582 / Mean I/σ(I) obs: 5.3

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.2→15 Å / Rfactor Rfree error: 0.009 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.308 1235 6.8 %random
Rwork0.266 ---
all-20605 --
obs-18169 88.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 95.768 Å2 / ksol: 0.32175 e/Å3
Displacement parametersBiso mean: 53.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.98 Å20 Å20 Å2
2---2.98 Å20 Å2
3---5.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1852 0 63 114 2029
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.25
X-RAY DIFFRACTIONc_dihedral_angle_d19.4
X-RAY DIFFRACTIONc_improper_angle_d0.94
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.393 160 6.5 %
Rwork0.36 2288 -
obs--72.3 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3BNG.para
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 15 Å / Rfactor obs: 0.266 / Rfactor Rfree: 0.308 / Rfactor Rwork: 0.266
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94
LS refinement shell
*PLUS
Rfactor Rfree: 0.393 / Rfactor Rwork: 0.36

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