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- PDB-8ghj: Crystal structure of human AQP2 T125M mutant -

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Basic information

Entry
Database: PDB / ID: 8ghj
TitleCrystal structure of human AQP2 T125M mutant
ComponentsAquaporin-2
KeywordsMEMBRANE PROTEIN / Aquaporin / water channel
Function / homology
Function and homology information


cellular response to water deprivation / renal water transport / glycerol transmembrane transporter activity / Passive transport by Aquaporins / glycerol transmembrane transport / lumenal side of membrane / water transmembrane transporter activity / cellular response to mercury ion / water transport / water channel activity ...cellular response to water deprivation / renal water transport / glycerol transmembrane transporter activity / Passive transport by Aquaporins / glycerol transmembrane transport / lumenal side of membrane / water transmembrane transporter activity / cellular response to mercury ion / water transport / water channel activity / metanephric collecting duct development / renal water homeostasis / transport vesicle membrane / cellular response to copper ion / actin filament organization / recycling endosome / Vasopressin regulates renal water homeostasis via Aquaporins / basolateral plasma membrane / protein homotetramerization / apical plasma membrane / perinuclear region of cytoplasm / Golgi apparatus / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Aquaporin transporter / Major intrinsic protein, conserved site / MIP family signature. / Major intrinsic protein / Major intrinsic protein / Aquaporin-like
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsHorsefield, S. / Hagstroemer, C.J.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council2017-06727 Sweden
The Crafoord Foundation20180916 Sweden
CitationJournal: Sci Rep / Year: 2023
Title: Structural and functional analysis of aquaporin-2 mutants involved in nephrogenic diabetes insipidus.
Authors: Hagstromer, C.J. / Hyld Steffen, J. / Kreida, S. / Al-Jubair, T. / Frick, A. / Gourdon, P. / Tornroth-Horsefield, S.
History
DepositionMar 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aquaporin-2
B: Aquaporin-2
C: Aquaporin-2
D: Aquaporin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,9026
Polymers100,6774
Non-polymers2252
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14470 Å2
ΔGint-148 kcal/mol
Surface area31810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.310, 118.310, 90.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number77
Space group name H-MP42
Space group name HallP4c
Symmetry operation#1: x,y,z
#2: -y,x,z+1/2
#3: y,-x,z+1/2
#4: -x,-y,z

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Components

#1: Protein
Aquaporin-2 / AQP-2 / ADH water channel / Aquaporin-CD / AQP-CD / Collecting duct water channel protein / WCH-CD ...AQP-2 / ADH water channel / Aquaporin-CD / AQP-CD / Collecting duct water channel protein / WCH-CD / Water channel protein for renal collecting duct


Mass: 25169.312 Da / Num. of mol.: 4 / Mutation: T125M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AQP2 / Production host: Komagataella pastoris (fungus) / References: UniProt: P41181
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20- 30% PEG400, Tris-HCl pH 8.5, 0.1M MgCl2, 0.1M NaCl, 0.025 M CdCl2 added to the drop only

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.977 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 3.9→50 Å / Num. obs: 22380 / % possible obs: 99.9 % / Redundancy: 21.3 % / Biso Wilson estimate: 215.48 Å2 / CC1/2: 0.99 / Net I/σ(I): 0.43
Reflection shellResolution: 3.9→3.99 Å / Num. unique obs: 1641 / CC1/2: 0.287

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Processing

Software
NameVersionClassification
MxCuBE1.17_3644data collection
PHENIX1.17_3644refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NEF

4nef


Resolution: 3.9→49.5 Å / SU ML: 0.5979 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.0154
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3131 2222 10.04 %
Rwork0.2881 19903 -
obs0.2903 22125 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 214.44 Å2
Refinement stepCycle: LAST / Resolution: 3.9→49.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6842 0 2 0 6844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00317006
X-RAY DIFFRACTIONf_angle_d0.87039578
X-RAY DIFFRACTIONf_chiral_restr0.05021161
X-RAY DIFFRACTIONf_plane_restr0.0031207
X-RAY DIFFRACTIONf_dihedral_angle_d18.23222352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9-3.990.40371260.3841108X-RAY DIFFRACTION87.64
3.99-4.080.32491430.33221265X-RAY DIFFRACTION99.15
4.08-4.180.38361350.31841210X-RAY DIFFRACTION99.56
4.18-4.290.34731420.31241300X-RAY DIFFRACTION99.86
4.29-4.420.32971360.30471222X-RAY DIFFRACTION99.85
4.42-4.560.2821420.3081263X-RAY DIFFRACTION99.86
4.56-4.720.33821480.29021265X-RAY DIFFRACTION100
4.73-4.910.31641340.29171267X-RAY DIFFRACTION100
4.91-5.140.33141380.27971260X-RAY DIFFRACTION100
5.14-5.410.33511380.30791247X-RAY DIFFRACTION100
5.41-5.750.36841480.28311250X-RAY DIFFRACTION100
5.75-6.190.3841320.30281258X-RAY DIFFRACTION100
6.19-6.810.28871460.2881255X-RAY DIFFRACTION100
6.81-7.790.26291310.2491259X-RAY DIFFRACTION99.86
7.8-9.80.24281460.22581245X-RAY DIFFRACTION100
9.81-49.50.34031370.32191229X-RAY DIFFRACTION97.78

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