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- PDB-8oee: Crystal structure of human AQP2 T126M mutant -

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Basic information

Entry
Database: PDB / ID: 8oee
TitleCrystal structure of human AQP2 T126M 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 / water transmembrane transporter activity / Passive transport by Aquaporins / lumenal side of membrane / glycerol transmembrane transport / cellular response to mercury ion / water transport / water channel activity ...cellular response to water deprivation / renal water transport / glycerol transmembrane transporter activity / water transmembrane transporter activity / Passive transport by Aquaporins / lumenal side of membrane / glycerol transmembrane transport / cellular response to mercury ion / water transport / water channel activity / metanephric collecting duct development / transport vesicle membrane / renal water homeostasis / cellular response to copper ion / actin filament organization / recycling endosome / Vasopressin regulates renal water homeostasis via Aquaporins / protein homotetramerization / basolateral plasma membrane / 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: 3.15 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: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water27015
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14560 Å2
ΔGint-142 kcal/mol
Surface area32720 Å2
Unit cell
Length a, b, c (Å)118.940, 118.940, 89.960
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: T126M
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 61.3 %
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: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.15→89.98 Å / Num. obs: 42680 / % possible obs: 99.77 % / Redundancy: 11.3 % / Biso Wilson estimate: 99 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.1
Reflection shellResolution: 3.15→3.36 Å / Num. unique obs: 3952 / CC1/2: 0.208

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIX1.20.1_4487refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→71.75 Å / SU ML: 0.6654 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.0807
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2843 2132 5 %
Rwork0.2504 40548 -
obs0.252 42680 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 124.36 Å2
Refinement stepCycle: LAST / Resolution: 3.15→71.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6928 0 2 15 6945
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00277092
X-RAY DIFFRACTIONf_angle_d0.63219692
X-RAY DIFFRACTIONf_chiral_restr0.04011175
X-RAY DIFFRACTIONf_plane_restr0.00641221
X-RAY DIFFRACTIONf_dihedral_angle_d3.96982
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.220.44441280.38612694X-RAY DIFFRACTION98.43
3.22-3.30.43631350.3812698X-RAY DIFFRACTION99.16
3.3-3.390.36141480.35942710X-RAY DIFFRACTION99.79
3.39-3.490.40431360.35652652X-RAY DIFFRACTION99.89
3.49-3.60.33561780.31882725X-RAY DIFFRACTION99.97
3.6-3.730.29321900.28312671X-RAY DIFFRACTION100
3.73-3.880.2991280.25132680X-RAY DIFFRACTION99.93
3.88-4.060.26041020.22582762X-RAY DIFFRACTION100
4.06-4.270.34781220.22292733X-RAY DIFFRACTION100
4.27-4.540.23361540.21212711X-RAY DIFFRACTION99.97
4.54-4.890.21531560.20572667X-RAY DIFFRACTION100
4.89-5.380.24111460.21742704X-RAY DIFFRACTION100
5.38-6.160.26381320.26382721X-RAY DIFFRACTION100
6.16-7.750.26171520.2372697X-RAY DIFFRACTION100
7.76-71.750.28211250.23212723X-RAY DIFFRACTION99.48
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)
11.51775999351.48828072544-1.616832690944.84353117109-0.1513587152996.806878409940.24198639567-1.35931294306-0.7340724209330.937324433338-0.453573253434-1.010293956540.657658646870.278981356220.2188666933280.768323837133-0.196149960371-0.2437839586551.328845179110.122598972980.82260644646920.8543117785-53.712697740921.6311379802
21.41327810337-0.369903920368-1.172878695234.842841065790.2369811070553.089657260530.452519600287-0.8307260636850.2091428430140.723700162353-0.5679138896-0.522125376917-0.4580520052690.03482319442160.06454436480830.918530038757-0.31330886073-0.1380212608561.11505509925-0.1476013923050.74155126617116.6691750441-41.127916454122.7687849568
32.55077870121-0.0573445933067-1.405739238655.655385718571.028806921655.58390255113-0.5281352636790.436748623031.69538371669-0.8275967890520.4438688428680.637957243351-1.5157450903-0.846327540856-0.175442086651.49387088329-0.06037223740820.1731951431510.8425299263310.160129424740.8314127627019.60020263808-29.606773615-14.3132613476
41.580049759160.22334253944-1.325380646563.07442788283-0.5387397561241.195334730010.588549103357-0.7142420336720.4675381658710.039486596340.106495625232-1.12477355693-0.7477619539360.9029521685360.5102060093032.32365908367-1.518789475530.886772313271.81251061589-0.6735206136441.8736791995132.466660623-26.108800875-3.47633037722
53.41286006321-0.400364782522-0.6903726217444.346330873870.9034616148824.34408005334-0.1349978572731.128882013340.80955473558-1.47511930031-0.215109494951-0.576181468733-1.255515007730.3242442125-0.01388577146780.999698790826-0.07354747337430.1101563663630.4575387255860.1455860600050.67896967649114.8160210848-36.3121849387-6.20813516801
65.18433327439-4.57410677787-2.881440158114.033617978242.559492793261.99733570746-0.4418083584361.592862471160.311109990573-2.35993809132-0.3950830040170.8715798611820.845957225291-1.03486567010.4318406179491.40622822828-0.3833145439640.08046600206241.273880556420.01069674029981.074091462858.64399356744-42.8366915612-20.7617379483
75.791273630770.8883706660922.808149822141.862892364973.042917687265.23972139565-0.3068477890230.2759800599960.953602692665-0.9590093563940.6601609051640.201519160849-0.742711920564-0.947773162512-0.8390814503521.95115974616-0.2251413937850.1793911791011.064909672110.4751475140571.0660782699912.6524609114-28.5170217842-20.0327129439
80.6428554101970.6023156588720.9937046742393.330065254570.5531275796161.5212322925-0.6019343376920.6012191102130.493491028227-0.1614587107730.285642892557-0.36912514034-0.6644158327021.98429872948-0.3055676022661.54904526535-0.7750380617870.09453477307782.008837845080.4550784282431.1153255370832.33475071-28.9999190582-15.117684024
92.9679274001-0.639130916742-1.806535970011.056884321270.488301783894.5436245083-0.253246736021-0.248496904646-0.369320185177-1.64492786282-0.19377420478-0.5647547205580.0584383382907-0.213134712590.2125620730431.51540349581-0.3164639472090.3688644322021.174228714660.02593269587660.80427993616721.102601824-47.7334314975-16.6411648811
104.398963807494.513586011423.260294869184.919323019493.357542317014.44684478286-0.26422179454-1.816510856771.26075982761-0.367547557337-1.550305361752.27918978326-0.379942035657-0.8390014082171.271875418721.99521262162-0.6762380071060.5212885470611.35403151388-0.7116275038722.160804086084.12723661621-52.4475495765-7.08899722953
113.32004318028-2.199764491260.6579493171292.141070883481.02561857573.33189933727-0.3274263461030.7256302439140.437340877233-1.00914122327-0.503218884346-0.460825760131-0.05804310474910.76112644051-0.1451111018061.25907284501-0.2909664381610.4691192451731.147766510060.229952039370.72656224552123.2144097729-42.7860776503-8.43641015905
124.455328469974.771818990011.023427221632.0017298312-2.337186990622.66576360545-0.1428625378890.7285177394440.223449970046-1.535538324390.544978614446-1.52556688589-0.7147152361791.717995697251.021326862481.9000957601-0.8446392315830.5178925737981.310697187050.02925572597841.6493439702725.331436342-31.617181552-20.5268605156
130.5401326676190.189983659975-0.913267394111.94735172934-0.5753961533522.49981804021-0.1942699880770.4189442619780.520419329378-0.6708761324380.545389190431-0.477773922594-1.109020541151.647255531710.9254051380992.41771778919-0.5905016594961.053753901811.502054715980.1318194329520.34386531311919.1518699743-46.6795562691-23.3077381364
145.96693977141-0.346965326514-2.696877571016.32383311701-5.439765386186.20462057191-0.4578400162920.577397205067-0.202209249444-0.9709838034970.5177792484991.034419055191.35270470633-1.16212927427-0.2574375353371.46104794781-0.1498151677350.7662785521720.715937446534-0.1167015499751.134705531455.80079752035-61.2083998917-20.2177432888
155.24997682644-0.7742732302092.502565464331.62352130791-0.7404246736843.066328662061.197944879831.717892487730.435936305236-1.10978078564-1.22203387151-0.8621991318881.781531960281.592383785440.4376666300933.129901195051.026303886661.158692286773.936386591371.077103270721.76409807796-3.20341276804-67.8197421919-32.6585813107
163.505951889231.23143230842-1.145733535383.97487689257-1.500609899632.85967244153-0.3200990295770.0495042631108-0.91417795845-1.193513949880.11069365398-1.80917888320.2451832239770.8827907221680.3993481645350.832985615554-0.02139618871710.4422250540050.936793590775-0.1117733102021.4461921109927.2342563405-58.4543148557-4.09714361318
170.17129580175-0.730269368807-0.8765074176325.899812694481.220990808587.04893019128-0.24055212818-0.596542448473-0.921142646354-0.00729664994727-0.0812502834965-0.5508929302310.307055263114-0.2135903778460.3746989829770.7036301492670.07917149130180.1225332709540.9460226154620.06563037893281.069451662519.1078150036-54.66602056456.15978085027
181.35656064988-0.2866968700520.5592700014761.085484149421.633525081933.308925764060.499200609791-0.281709563552-1.379404222910.0113579777119-0.202051664423-1.432318473450.4584091864510.504263065983-0.1337658344290.5553420535010.171805998270.0714508249511.06180159010.2046801169411.4418734477924.4933875607-69.3365539645.24410118934
194.0490926822-0.1268167191741.108688418125.488104063130.08872162019535.027594006840.7137374762190.415080760575-0.159741047761.50235498813-1.275538397711.77674850770.582307910603-0.686165178407-0.07752932996221.23820786999-0.2939940006280.2017119737891.13469748129-0.6041547209311.321951304134.7145372867-28.597032374119.2427984816
202.362480439461.92308388779-1.868165326534.955979612940.4391218207214.254615669410.490637231199-0.584172413693-0.6753913233450.718377591742-0.302590492469-1.25462430308-0.6184527402911.09756805933-0.1327941320550.707444357352-0.191643545337-0.0005427492734710.68469780912-0.2105343228841.2584503040819.4936847718-32.510124107711.3849692702
214.973156795790.471221054932-3.82011764220.177329719447-0.4337313697576.896949520970.279037757979-1.25416269952.0869529482-0.509155455094-0.7649137680451.05711278072-1.97932459846-1.519984885040.3641922553181.673850316320.05560744925390.06316151039290.789972490077-0.4647462954431.61440804343.83007194039-22.407797722512.7521371095
222.044091231980.824349655838-0.921777930792.72130242405-2.128557389731.621691517710.217931790202-0.5588713413982.25197423515-0.545447139394-0.508129725193-0.0929558367214-0.8152466656370.6595124347960.4131646390451.20272620681-0.2244728455430.02177689135820.822491490508-0.1009762225321.5162761768418.6390078167-21.20353082445.07774457242
237.06234106612-6.41729999857.034519541835.82456185778-6.399856755597.008156308760.6210169105811.33201559421-1.1121208588-1.771488291860.572894609042.38766758526-0.314754794786-0.175982223277-0.5388586047410.9886445574980.248586657071-0.2559592295381.05157314437-0.1684344462571.51532490539-2.13385997428-39.81175381520.254805031785
241.5564653474-2.029165832210.31668237383.009883104340.6459988217572.98227700451-0.151104954563-1.022936510671.4250368113-0.668912411702-0.2758481975460.396316310386-0.3920017342281.07238130980.5098296493560.8109178175-0.2711801177790.1097183065670.731984663994-0.2185604256240.93940219900417.4502349668-29.90530386011.49539017803
251.3777461019-0.865982399583-0.05697240445124.701961984912.137564766661.54213737187-0.4189920734990.09580770472821.608739198740.225052023141-0.1128662188450.208255321566-1.725122860111.497258254850.204273482241.44810846247-0.4261397485770.08549740076591.278341809-0.4251430869031.7645636809817.9200355747-16.359464845111.3778439027
261.90027623298-1.4186747186-2.18279617893.08866371726-0.8691712499625.547537089060.528516310585-0.1759888489891.41332518004-1.68666587034-0.5370652264011.15328744605-0.2919225912320.8288163014770.1363978633351.56997669830.0533570969459-0.2517601772560.82085527455-0.4166634821462.097570343456.53629325148-18.2963113503-0.384817796337
272.7849044362-1.5783238482-2.063277022072.8065502044.089306716866.01677461135-1.98789525117-0.0941088873012-1.128613411641.333094168770.124339197712-0.2612626922030.542832686851-0.9202189921911.06876597392.46271588317-0.905046834785-0.4585525414951.276390402930.674430976841.38711987614-11.6495939454-31.6805292683-9.99249472986
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 107 )AA2 - 1071 - 106
22chain 'A' and (resid 108 through 240 )AA108 - 240107 - 239
33chain 'B' and (resid 6 through 31 )BB6 - 311 - 26
44chain 'B' and (resid 32 through 40 )BB32 - 4027 - 35
55chain 'B' and (resid 41 through 63 )BB41 - 6336 - 58
66chain 'B' and (resid 64 through 82 )BB64 - 8259 - 77
77chain 'B' and (resid 83 through 107 )BB83 - 10778 - 102
88chain 'B' and (resid 108 through 126 )BB108 - 126103 - 121
99chain 'B' and (resid 127 through 149 )BB127 - 149122 - 144
1010chain 'B' and (resid 150 through 159 )BB150 - 159145 - 154
1111chain 'B' and (resid 160 through 179 )BB160 - 179155 - 174
1212chain 'B' and (resid 180 through 200 )BB180 - 200175 - 195
1313chain 'B' and (resid 201 through 221 )BB201 - 221196 - 216
1414chain 'B' and (resid 222 through 229 )BB222 - 229217 - 224
1515chain 'B' and (resid 230 through 238 )BB230 - 238225 - 233
1616chain 'C' and (resid 6 through 148 )CC6 - 1481 - 143
1717chain 'C' and (resid 149 through 179 )CC149 - 179144 - 174
1818chain 'C' and (resid 180 through 241 )CC180 - 241175 - 236
1919chain 'D' and (resid 2 through 31 )DD2 - 311 - 30
2020chain 'D' and (resid 32 through 63 )DD32 - 6331 - 62
2121chain 'D' and (resid 64 through 105 )DD64 - 10563 - 104
2222chain 'D' and (resid 106 through 148 )DD106 - 148105 - 147
2323chain 'D' and (resid 149 through 159 )DD149 - 159148 - 158
2424chain 'D' and (resid 160 through 179 )DD160 - 179159 - 178
2525chain 'D' and (resid 180 through 200 )DD180 - 200179 - 199
2626chain 'D' and (resid 201 through 221 )DD201 - 221200 - 220
2727chain 'D' and (resid 222 through 233 )DD222 - 233221 - 232

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