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- PDB-4oj2: The structure of aquaporin -

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Basic information

Entry
Database: PDB / ID: 4oj2
TitleThe structure of aquaporin
ComponentsAquaporin-2
KeywordsTRANSPORT PROTEIN / aquaporin-2 / water transport simulations / c-terminal alpha helix / Structural Genomics / Protein Structure Initiative / Transcontinental EM Initiative for Membrane Protein Structure / TEMIMPS / NPA motif / Water Channel / Membrane / PSI-Biology
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 / Resolution: 3.05 Å
AuthorsVahedi-Faridi, A. / Lodowski, D. / Engel, A. / Transcontinental EM Initiative for Membrane Protein Structure (TEMIMPS)
CitationJournal: To be Published
Title: The structure of aquaporin
Authors: Vahedi-Faridi, A. / Lodowski, D. / Schenk, A. / Kaptan, S. / De groot, B. / Walz, T. / Engel, A.
History
DepositionJan 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Aquaporin-2


Theoretical massNumber of molelcules
Total (without water)29,1711
Polymers29,1711
Non-polymers00
Water45025
1
X: Aquaporin-2

X: Aquaporin-2

X: Aquaporin-2

X: Aquaporin-2


Theoretical massNumber of molelcules
Total (without water)116,6834
Polymers116,6834
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area13540 Å2
ΔGint-141 kcal/mol
Surface area40470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.717, 95.717, 79.058
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-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: 29170.740 Da / Num. of mol.: 1 / Mutation: S256A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AQP2 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P41181
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 3.1 Å3/Da / Density % sol: 60.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 30% PEG 400, 0.1M sodium chloride, 0.1M MOPS, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 8, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.05→79.07 Å / Num. all: 7130 / Num. obs: 7153 / % possible obs: 99.68 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 13.8 % / Net I/σ(I): 38.8
Reflection shellResolution: 3.05→3.29 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→79.07 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.895 / SU B: 56.229 / SU ML: 0.465 / Cross valid method: THROUGHOUT / ESU R Free: 0.479 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29897 300 4 %RANDOM
Rwork0.25707 ---
obs0.25893 7130 99.68 %-
all-7153 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 150.323 Å2
Baniso -1Baniso -2Baniso -3
1--2.58 Å20 Å20 Å2
2---2.58 Å20 Å2
3---5.15 Å2
Refinement stepCycle: LAST / Resolution: 3.05→79.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1890 0 0 25 1915
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0191935
X-RAY DIFFRACTIONr_bond_other_d00.021898
X-RAY DIFFRACTIONr_angle_refined_deg0.6931.9612643
X-RAY DIFFRACTIONr_angle_other_deg0.49834332
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4855252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.36722.63972
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.98115287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0571512
X-RAY DIFFRACTIONr_chiral_restr0.0380.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212200
X-RAY DIFFRACTIONr_gen_planes_other00.02454
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7449.6621011
X-RAY DIFFRACTIONr_mcbond_other2.7459.6561010
X-RAY DIFFRACTIONr_mcangle_it4.40614.4751262
X-RAY DIFFRACTIONr_mcangle_other4.40414.4821263
X-RAY DIFFRACTIONr_scbond_it2.2819.934924
X-RAY DIFFRACTIONr_scbond_other2.289.939925
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.79214.811382
X-RAY DIFFRACTIONr_long_range_B_refined7.08181.0242558
X-RAY DIFFRACTIONr_long_range_B_other7.0881.0512559
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.048→3.127 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 32 -
Rwork0.34 499 -
obs--99.81 %
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)
14.34030.1731-0.58734.17691.25311.46240.0243-0.0346-0.66560.13820.02190.39660.4562-0.2682-0.04610.3771-0.0494-0.06920.32020.12060.2244-9.249530.58424.024
29.5121-3.20167.80891.1322-2.56866.9311-0.15670.3668-0.74630.04480.06080.451-0.5538-0.00910.09591.4962-0.0388-0.15481.4089-0.03741.4025-38.877338.9374-11.697
33.2747-1.8382-0.64131.23070.92481.8211-0.09580.0526-0.63870.1149-0.18020.40940.2986-0.2680.2760.5058-0.12460.06740.4028-0.06760.2464-8.990329.962223.9785
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1X5 - 31
2X-RAY DIFFRACTION1X32 - 41
3X-RAY DIFFRACTION1X42 - 108
4X-RAY DIFFRACTION1X109 - 126
5X-RAY DIFFRACTION1X127 - 149
6X-RAY DIFFRACTION1X150 - 160
7X-RAY DIFFRACTION1X161 - 221
8X-RAY DIFFRACTION2X222 - 233
9X-RAY DIFFRACTION2X234 - 257
10X-RAY DIFFRACTION3X301 - 325

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