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- PDB-6qzj: Crystal structure of human Aquaporin 7 at 2.2 A resolution -

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Basic information

Entry
Database: PDB / ID: 6qzj
TitleCrystal structure of human Aquaporin 7 at 2.2 A resolution
ComponentsAquaporin-7
KeywordsMEMBRANE PROTEIN / Aquaglyceroporin / glycerol channel
Function / homology
Function and homology information


Transport of glycerol from adipocytes to the liver by Aquaporins / glycerol channel activity / urea transmembrane transporter activity / Passive transport by Aquaporins / glycerol transmembrane transport / water transport / water channel activity / lipid droplet / cytoplasmic vesicle membrane / cell-cell junction ...Transport of glycerol from adipocytes to the liver by Aquaporins / glycerol channel activity / urea transmembrane transporter activity / Passive transport by Aquaporins / glycerol transmembrane transport / water transport / water channel activity / lipid droplet / cytoplasmic vesicle membrane / cell-cell junction / cell cortex / basolateral plasma membrane / plasma membrane / cytoplasm
Similarity search - Function
Glycerol uptake facilitator protein / Glycerol uptake facilitator protein. / Major intrinsic protein / Major intrinsic protein / Aquaporin-like / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Aquaporin-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
Authorsde Mare, S.W.-H. / Venskutonyte, R. / Eltschkner, S. / Lindkvist-Petersson, K.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Structure / Year: 2020
Title: Structural Basis for Glycerol Efflux and Selectivity of Human Aquaporin 7.
Authors: de Mare, S.W. / Venskutonyte, R. / Eltschkner, S. / de Groot, B.L. / Lindkvist-Petersson, K.
History
DepositionMar 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Feb 12, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aquaporin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,96914
Polymers26,7661
Non-polymers1,20313
Water21612
1
A: Aquaporin-7
hetero molecules

A: Aquaporin-7
hetero molecules

A: Aquaporin-7
hetero molecules

A: Aquaporin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,87756
Polymers107,0654
Non-polymers4,81252
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area27140 Å2
ΔGint-211 kcal/mol
Surface area28950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.761, 86.761, 83.544
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Aquaporin-7 / AQP-7 / Aquaglyceroporin-7 / Aquaporin adipose / AQPap / Aquaporin-7-like


Mass: 26766.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AQP7, AQP7L, AQP9 / Production host: Komagataella pastoris (fungus) / References: UniProt: O14520
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.94 Å3/Da / Density % sol: 58.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 85 mM Tris pH 8.0, 37 % v/v PEG 200 and 0.80 % v/v OG

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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: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.2→61.35 Å / Num. obs: 15584 / % possible obs: 98.8 % / Redundancy: 3.3 % / CC1/2: 1 / Rmerge(I) obs: 0.027 / Rpim(I) all: 0.016 / Rrim(I) all: 0.032 / Net I/σ(I): 17.2
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.673 / Num. unique obs: 1364 / CC1/2: 0.788 / Rpim(I) all: 0.418 / Rrim(I) all: 0.797 / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.3data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6f7h

6f7h


Resolution: 2.2→41.772 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 35.48
RfactorNum. reflection% reflection
Rfree0.2432 812 5.23 %
Rwork0.2087 --
obs0.2105 15532 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 170.71 Å2 / Biso mean: 86.4197 Å2 / Biso min: 55.03 Å2
Refinement stepCycle: final / Resolution: 2.2→41.772 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1868 0 76 12 1956
Biso mean--102.46 76.41 -
Num. residues----245
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.33780.42431260.36662454258099
2.3378-2.51830.32391620.29232422258498
2.5183-2.77170.3011020.25152490259299
2.7717-3.17260.26731570.24142440259799
3.1726-3.99670.26961240.20612478260298
3.9967-41.77950.20661410.18072436257796
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)
13.99-0.2230.92173.43461.22740.6675-0.10850.23030.0739-0.36320.01920.5460.2597-0.15340.17350.8658-0.0212-0.0850.9056-0.00260.37227.198240.67519.7833
21.18440.0987-0.25657.19130.05350.0515-0.15690.0737-0.38870.54510.2240.0487-0.01760.17320.14350.9264-0.10950.02160.97020.06820.473724.400227.098532.563
31.871-0.0877-0.14635.17041.49430.4332-0.09180.70240.0736-0.63760.09230.6874-0.4719-0.43750.04210.5795-0.0887-0.1751.0397-0.07180.495317.360137.654217.8526
42.87551.9057-1.36443.3238-1.47713.5824-0.37031.55880.0154-2.12930.27760.5570.3823-0.1728-0.41741.83410.1271-0.52922.0224-0.35320.715719.871437.284-1.9343
53.67430.3380.6323.35591.18120.80390.30080.8069-0.0103-0.9617-0.04340.4520.4671-0.62850.23621.40160.0123-0.25671.2868-0.20910.66226.5928.06655.8427
66.13920.25742.14852.9248-0.35492.82760.1957-0.0794-0.7714-0.2079-0.02990.25820.76960.195-0.28471.0533-0.0552-0.09450.741-0.02320.442833.283722.0620.9769
75.2676-1.15362.57262.32660.57551.8743-0.1512-0.8594-0.69180.4170.93550.20150.1788-0.28190.05991.05570.02440.08531.10380.08960.43640.128232.161138.6499
84.78951.10831.35362.4081.45062.1307-0.23260.4032-0.3374-0.1193-0.03860.4355-0.0159-0.25880.10951.0454-0.0914-0.05371.0168-0.07570.480226.951532.198816.1135
94.1074-1.3014-0.89444.84430.23333.3748-0.2721.1347-0.4353-0.6784-0.09710.561-0.1640.64670.25150.8124-0.1153-0.01190.6048-0.00270.469826.174420.507719.3057
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 34 through 85 )A34 - 85
2X-RAY DIFFRACTION2chain 'A' and (resid 86 through 108 )A86 - 108
3X-RAY DIFFRACTION3chain 'A' and (resid 109 through 142 )A109 - 142
4X-RAY DIFFRACTION4chain 'A' and (resid 143 through 154 )A143 - 154
5X-RAY DIFFRACTION5chain 'A' and (resid 155 through 167 )A155 - 167
6X-RAY DIFFRACTION6chain 'A' and (resid 168 through 190 )A168 - 190
7X-RAY DIFFRACTION7chain 'A' and (resid 191 through 201 )A191 - 201
8X-RAY DIFFRACTION8chain 'A' and (resid 202 through 243 )A202 - 243
9X-RAY DIFFRACTION9chain 'A' and (resid 244 through 278 )A244 - 278

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