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- PDB-4nef: X-ray structure of human Aquaporin 2 -

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Basic information

Entry
Database: PDB / ID: 4nef
TitleX-ray structure of human Aquaporin 2
ComponentsAquaporin-2
KeywordsMEMBRANE PROTEIN / water channel / cadmium binding
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
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å
AuthorsFrick, A. / Eriksson, U. / Mattia, F.D. / Oberg, F. / Hedfalk, K. / Neutze, R. / Grip, W.D. / Deen, P.M.T. / Tornroth-horsefield, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: X-ray structure of human aquaporin 2 and its implications for nephrogenic diabetes insipidus and trafficking
Authors: Frick, A. / Eriksson, U.K. / de Mattia, F. / Oberg, F. / Hedfalk, K. / Neutze, R. / de Grip, W.J. / Deen, P.M. / Tornroth-Horsefield, S.
History
DepositionOct 29, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references

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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)101,2367
Polymers100,9454
Non-polymers2903
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14800 Å2
ΔGint-178 kcal/mol
Surface area32690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.110, 119.110, 90.621
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42
Components on special symmetry positions
IDModelComponents
11B-312-

HOH

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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: 25236.336 Da / Num. of mol.: 4 / Fragment: UNP residues 1-241 / Mutation: W2S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AQP2 / Production host: Pichia 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
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.32 %
Crystal growTemperature: 277 K / pH: 8
Details: 22% PEG400, 0.1M Tris, 0.1M NaCl, 0.15M MgCl2. 0.1M CdCl2, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 29, 2013
RadiationMonochromator: CHANNEL CUT ESRF MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.75→119.11 Å / Num. obs: 33049 / % possible obs: 99.9 % / Redundancy: 4.2 % / Biso Wilson estimate: 74.49 Å2 / Rsym value: 0.089 / Net I/σ(I): 9.9
Reflection shellResolution: 2.85→3 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.735 / Mean I/σ(I) obs: 1 / Rsym value: 0.735 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.21data scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→49.96 Å / Cor.coef. Fo:Fc: 0.9042 / Cor.coef. Fo:Fc free: 0.8953 / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 1.184 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2251 1674 5.07 %RANDOM
Rwork0.2019 ---
obs0.203 33049 99.82 %-
all-29716 --
Displacement parametersBiso mean: 91.37 Å2
Baniso -1Baniso -2Baniso -3
1-2.9148 Å20 Å20 Å2
2--2.9148 Å20 Å2
3----5.8297 Å2
Refine analyzeLuzzati coordinate error obs: 0.485 Å
Refinement stepCycle: LAST / Resolution: 2.75→49.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6924 0 3 59 6986
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0097106HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.139716HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2240SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes99HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1080HARMONIC5
X-RAY DIFFRACTIONt_it7106HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.23
X-RAY DIFFRACTIONt_other_torsion20.63
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion948SEMIHARMONIC25
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8937SEMIHARMONIC4
LS refinement shellResolution: 2.75→2.83 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2468 142 5 %
Rwork0.2241 2699 -
all0.2252 2841 -
obs--99.82 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.22851.2667-0.34394.4531-0.31692.77480.4858-1.0885-0.14710.9138-0.44330.83010.3144-0.648-0.0425-0.2256-0.3040.14130.24790.0777-0.335641.1766106.46919.1837
22.42960.84850.75673.65450.1733.8758-0.06650.7001-0.5655-1.08850.22750.26380.6425-0.2933-0.1610.1902-0.201-0.304-0.1795-0.1326-0.300843.232699.0133-19.4041
33.50520.6424-0.14332.170.47542.47550.0735-0.16730.6416-0.67-0.11341.0885-0.3153-0.7270.04-0.21450.0871-0.2845-0.1095-0.02020.140834.3536120.676-3.5598
41.60380.64160.41214.73170.02513.3630.2542-0.4931-1.08850.0596-0.1613-0.14591.035-0.1807-0.09290.0074-0.2036-0.188-0.33560.26820.119349.572185.03484.6615
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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