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- PDB-6qf5: X-Ray structure of human Aquaporin 2 crystallized on a silicon chip -

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Basic information

Entry
Database: PDB / ID: 6qf5
TitleX-Ray structure of human Aquaporin 2 crystallized on a silicon chip
ComponentsAquaporin-2
KeywordsMEMBRANE PROTEIN / human Aquaporin 2 / serial crystallography / XFEL / on-chip crystallization
Function / homology
Function and homology information


renal water transport / cellular response to water deprivation / glycerol transmembrane transporter activity / water transmembrane transporter activity / lumenal side of membrane / Passive transport by Aquaporins / glycerol transmembrane transport / cellular response to mercury ion / water transport / water channel activity ...renal water transport / cellular response to water deprivation / glycerol transmembrane transporter activity / water transmembrane transporter activity / lumenal side of membrane / Passive transport by Aquaporins / 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 / 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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsLieske, J. / Cerv, M. / Kreida, S. / Barthelmess, M. / Fischer, P. / Pakendorf, T. / Yefanov, O. / Mariani, V. / Seine, T. / Ross, B.H. ...Lieske, J. / Cerv, M. / Kreida, S. / Barthelmess, M. / Fischer, P. / Pakendorf, T. / Yefanov, O. / Mariani, V. / Seine, T. / Ross, B.H. / Crosas, E. / Lorbeer, O. / Burkhardt, A. / Lane, T.J. / Guenther, S. / Bergtholdt, J. / Schoen, S. / Tornroth-Horsefield, S. / Chapman, H.N. / Meents, A.
Funding support Germany, Sweden, United States, 6items
OrganizationGrant numberCountry
European Research Council609920 Germany
European UnionHorizon 2020, No. 654220 Germany
German Federal Ministry for Education and Research05K2018-2017-06727MXD Germany
Swedish Research Council2010-5208 Sweden
Swedish Research Council2012-2849 Sweden
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
CitationJournal: Iucrj / Year: 2019
Title: On-chip crystallization for serial crystallography experiments and on-chip ligand-binding studies.
Authors: Lieske, J. / Cerv, M. / Kreida, S. / Komadina, D. / Fischer, J. / Barthelmess, M. / Fischer, P. / Pakendorf, T. / Yefanov, O. / Mariani, V. / Seine, T. / Ross, B.H. / Crosas, E. / Lorbeer, O. ...Authors: Lieske, J. / Cerv, M. / Kreida, S. / Komadina, D. / Fischer, J. / Barthelmess, M. / Fischer, P. / Pakendorf, T. / Yefanov, O. / Mariani, V. / Seine, T. / Ross, B.H. / Crosas, E. / Lorbeer, O. / Burkhardt, A. / Lane, T.J. / Guenther, S. / Bergtholdt, J. / Schoen, S. / Tornroth-Horsefield, S. / Chapman, H.N. / Meents, A.
History
DepositionJan 9, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)101,2837
Polymers100,9454
Non-polymers3373
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14560 Å2
ΔGint-150 kcal/mol
Surface area31190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.200, 122.200, 94.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number77
Space group name H-MP42

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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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AQP2 / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: P41181
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
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: 3.48 Å3/Da / Density % sol: 64.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Tris pH 8.5, 0.1M sodium chloride, 0.1M magnesium chloride, 22-25% PEG 400, cadmium chloride

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.367 Å
DetectorType: CS-PAD XPP / Detector: PIXEL / Date: Nov 13, 2016 / Frequency: 120
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.367 Å / Relative weight: 1
ReflectionResolution: 3.7→37.38 Å / Num. obs: 14866 / % possible obs: 99.97 % / Redundancy: 28.1 % / Biso Wilson estimate: 104.8 Å2 / CC1/2: 0.783 / R split: 0.437 / Net I/σ(I): 2.32
Reflection shellResolution: 3.7→3.76 Å / Redundancy: 17.7 % / Mean I/σ(I) obs: 0.92 / Num. unique obs: 1462 / CC1/2: 0.105 / R split: 1.538 / % possible all: 99.93
Serial crystallography measurementCollection time total: 0.5 hours / Focal spot size: 1 µm2 / Pulse duration: 60 fsec. / Pulse photon energy: 9.07 keV
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetDescription: on-chip crystallization / Motion control: Roadrunner II
Sample dehydration prevention: humidified helium stream in closed chamber
Sample holding: single crystalline silicon chip / Sample solvent: none, naked crystals / Support base: aluminum support
Serial crystallography data reductionCrystal hits: 3377 / Frames total: 137476 / Lattices indexed: 2723

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Processing

Software
NameVersionClassification
PHENIX1.10.1-2155_9999refinement
Coot0.8.2model building
PHASERphasing
PDB_EXTRACT3.24data extraction
CrystFELdata reduction
CrystFELdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NEF

4nef


Resolution: 3.7→33.892 Å / SU ML: 0.69 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.12
RfactorNum. reflection% reflection
Rfree0.3357 1488 10.05 %
Rwork0.2818 --
obs0.2873 14805 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 232.76 Å2 / Biso mean: 105.453 Å2 / Biso min: 28.76 Å2
Refinement stepCycle: final / Resolution: 3.7→33.892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6608 0 3 4 6615
Biso mean--130.65 77.61 -
Num. residues----901
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046774
X-RAY DIFFRACTIONf_angle_d0.7619277
X-RAY DIFFRACTIONf_chiral_restr0.041129
X-RAY DIFFRACTIONf_plane_restr0.0071168
X-RAY DIFFRACTIONf_dihedral_angle_d13.4393880
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.7002-3.81940.42021270.40031110123792
3.8194-3.95580.40741320.32651219135199
3.9558-4.11390.33461320.298111921324100
4.1139-4.30080.3631400.288612171357100
4.3008-4.5270.29391370.273912141351100
4.527-4.80990.30481340.2612211355100
4.8099-5.18010.32471430.24512041347100
5.1801-5.69920.35191320.276912281360100
5.6992-6.51870.37691340.345912201354100
6.5187-8.19370.31631380.274812321370100
8.1937-33.89360.32051390.261412601399100
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)
10.03330.0064-0.00950.0962-0.07940.1812-0.0459-0.04160.0361-0.2674-0.2360.0096-0.1305-0.2377-0.47531.09230.5497-0.22470.90111.5052-0.137253.578432.3754-7.3668
20.56430.1498-0.00430.42290.25690.2834-0.1107-0.0545-0.04750.0792-0.0599-0.0688-0.03420.0854-0.12540.52990.7416-0.2832.47260.22092.379827.36932.1186-1.0885
30.12180.14730.22270.1650.25910.3884-0.21420.04830.5645-0.61410.06140.9945-0.576-0.2437-0.05130.43870.11020.16130.72170.24790.877947.334325.97681.0929
40.466-0.34980.44912.79430.76880.92630.36820.070.07520.0447-0.0702-0.42820.35540.20550.31591.1906-0.01460.37380.26250.25361.750661.43336.4455.2407
50.0731-0.1275-0.28850.42680.49211.03940.19610.3216-0.0414-0.2315-0.28740.233-0.5521-0.5005-0.06321.85690.09340.26020.89150.33831.249752.188139.0467-7.4816
60.0334-0.02860.0090.0175-0.0038-0.0029-0.1318-0.18050.11820.10150.18150.1554-0.0227-0.1962-0.04491.5151.4458-0.52551.43080.49781.598432.421140.0679-8.2467
70.2231-0.1635-0.32640.4037-0.3351.72470.56060.06010.31110.18750.21910.2526-0.9407-0.05580.75270.90970.08150.12960.2803-0.29391.674846.238939.067713.152
80.1617-0.31360.05380.6086-0.08710.1926-0.0338-0.00050.14630.2256-0.0011-0.2127-0.0941-0.0397-0.0221.7937-0.1736-0.25451.5568-0.19430.536662.825219.92411.3296
90.09980.1142-0.15710.1107-0.15190.20480.2871-0.64620.61540.5530.04690.0818-1.027-1.07050.00770.81330.3044-0.05820.76440.04760.711643.521330.223710.2783
100.23980.193-0.19590.1648-0.20661.16260.16680.01610.36730.35670.6152-0.4413-0.2842-0.60530.80221.58210.0694-0.18530.48640.32371.772249.226643.13026.7968
110.49140.9707-0.03481.9165-0.0644-0.0011-0.106-0.1151-0.15850.07880.0179-0.33140.3050.5895-0.07091.9954-0.0958-0.44711.21980.0170.451171.009628.650322.5582
120.85480.22740.14841.84421.77381.8587-0.2879-0.5765-0.51661.99510.54720.79660.705-0.47340.57210.2476-0.17050.96950.6130.50191.240136.81180.162919.0754
130.4766-0.1631-0.65990.2422-0.11881.3918-0.63690.2684-0.5740.2185-0.33011.84530.2639-1.6425-0.06340.73150.04670.16571.0072-0.46231.917527.72141.28726.3438
140.3896-0.55060.12871.1818-0.22630.0414-0.62040.3711-1.26230.24270.28791.7150.0933-0.0418-0.03030.9211-0.08730.1991.2705-0.19171.460137.64823.11348.0378
150.8354-0.5351-0.29993.1121-1.50781.71450.4301-0.0254-0.62110.37110.32010.52630.3276-0.10640.880.7455-0.1386-0.2111.0557-0.32780.978137.6988-10.9984.4254
160.30370.5646-0.53291.8804-1.37941.12690.14180.5279-0.3663-0.7088-0.2408-0.20410.84590.8459-0.08240.598-0.0092-0.17691.5138-0.30910.693840.75511.1596-10.5454
170.62880.88610.02651.2927-0.20210.30920.14390.63450.8347-0.56680.26271.4421-0.064-0.50090.18610.94160.2351-0.32841.1131-0.19650.850439.35098.5698-9.7709
180.60910.2868-0.10552.84230.85041.48290.41981.28120.7965-1.3036-1.45371.339-0.9699-0.1027-2.13670.92830.6213-0.52191.2910.5495-0.049640.86918.9907-11.9557
190.54870.4523-0.3480.7424-0.08410.3934-0.2611-1.25790.71450.70450.2725-0.225-0.8946-0.40670.01381.03490.28510.16230.9265-0.1740.906247.243525.818523.8662
203.7183-0.35461.05930.5779-0.40250.50040.1999-0.5358-0.88740.5424-0.00510.9654-1.3781-0.78940.22111.77320.2380.32981.0457-0.5061.357939.824831.48829.8679
210.53510.06960.16140.2937-0.33460.5051-0.1504-0.49990.06360.60590.07220.6748-0.3746-0.99520.35510.74660.19641.26531.0839-0.72540.588939.617311.925728.8481
220.005-0.00690.00560.0049-0.00560.00650.2461-0.2091-0.24920.12010.0897-0.2630.12870.16230.00011.36290.32080.02771.2570.12751.349557.62657.048118.9016
230.3533-0.00690.10070.05450.24550.9505-0.3056-0.69790.59631.02130.29110.2887-1.0797-0.8763-0.06341.25330.36620.93660.8728-0.13671.3136.722822.795326.4644
240.0305-0.02-0.0230.2737-0.14760.2765-0.3263-0.17420.11420.1646-0.06510.1304-0.16220.0657-0.8572.66620.63411.68640.99080.49590.95144.03710.475634.5688
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 32 )A5 - 32
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 40 )A33 - 40
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 63 )A41 - 63
4X-RAY DIFFRACTION4chain 'A' and (resid 64 through 83 )A64 - 83
5X-RAY DIFFRACTION5chain 'A' and (resid 84 through 107 )A84 - 107
6X-RAY DIFFRACTION6chain 'A' and (resid 108 through 117 )A108 - 117
7X-RAY DIFFRACTION7chain 'A' and (resid 118 through 148 )A118 - 148
8X-RAY DIFFRACTION8chain 'A' and (resid 149 through 159 )A149 - 159
9X-RAY DIFFRACTION9chain 'A' and (resid 160 through 179 )A160 - 179
10X-RAY DIFFRACTION10chain 'A' and (resid 180 through 221 )A180 - 221
11X-RAY DIFFRACTION11chain 'A' and (resid 222 through 232 )A222 - 232
12X-RAY DIFFRACTION12chain 'B' and (resid 5 through 106 )B5 - 106
13X-RAY DIFFRACTION13chain 'B' and (resid 107 through 148 )B107 - 148
14X-RAY DIFFRACTION14chain 'B' and (resid 149 through 193 )B149 - 193
15X-RAY DIFFRACTION15chain 'B' and (resid 194 through 238 )B194 - 238
16X-RAY DIFFRACTION16chain 'C' and (resid 5 through 31 )C5 - 31
17X-RAY DIFFRACTION17chain 'C' and (resid 32 through 107 )C32 - 107
18X-RAY DIFFRACTION18chain 'C' and (resid 108 through 226 )C108 - 226
19X-RAY DIFFRACTION19chain 'D' and (resid 7 through 82 )D7 - 82
20X-RAY DIFFRACTION20chain 'D' and (resid 83 through 126 )D83 - 126
21X-RAY DIFFRACTION21chain 'D' and (resid 127 through 148 )D127 - 148
22X-RAY DIFFRACTION22chain 'D' and (resid 149 through 159 )D149 - 159
23X-RAY DIFFRACTION23chain 'D' and (resid 160 through 200 )D160 - 200
24X-RAY DIFFRACTION24chain 'D' and (resid 201 through 226 )D201 - 226

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