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- PDB-8vvx: Human Aquaporin 2 from 2D electron diffraction data -

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Basic information

Entry
Database: PDB / ID: 8vvx
TitleHuman Aquaporin 2 from 2D electron diffraction data
ComponentsAquaporin-2
KeywordsMEMBRANE PROTEIN / aquaporin / aquaglyceroporin / 2D crystallography / Structural Genomics / PSI-2 / Protein Structure Initiative / Transcontinental EM Initiative for Membrane Protein Structure / TEMIMPS
Function / homology
Function and homology information


cellular response to water deprivation / renal water transport / glycerol transmembrane transporter activity / lumenal side of membrane / water transmembrane transporter activity / Passive transport by Aquaporins / 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 / lumenal side of membrane / water transmembrane transporter activity / 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
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)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 2.6 Å
AuthorsVahedi-Faridi, A. / Lodowski, D.T. / Engel, A. / Transcontinental EM Initiative for Membrane Protein Structure (TEMIMPS)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5U54GM094598-04 United States
CitationJournal: To Be Published
Title: Human Aquaporin 2 from 2D electron diffraction data
Authors: Vahedi-Faridi, A. / Lodowski, D.T. / Engel, A.
History
DepositionJan 31, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Aquaporin-2
Y: Aquaporin-2
A: Aquaporin-2
B: Aquaporin-2


Theoretical massNumber of molelcules
Total (without water)106,7924
Polymers106,7924
Non-polymers00
Water00
1
X: Aquaporin-2
Y: Aquaporin-2
A: Aquaporin-2
B: Aquaporin-2

X: Aquaporin-2
Y: Aquaporin-2
A: Aquaporin-2
B: Aquaporin-2

X: Aquaporin-2
Y: Aquaporin-2
A: Aquaporin-2
B: Aquaporin-2


Theoretical massNumber of molelcules
Total (without water)320,37512
Polymers320,37512
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2
Buried area14740 Å2
ΔGint-117 kcal/mol
Surface area36820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.700, 94.700, 250.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2212

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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: 26697.877 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AQP2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P41181
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: electron crystallography
Crystal symmetry∠γ: 90 ° / C sampling length: 250 Å / A: 94.7 Å / B: 94.7 Å / C: 250 Å / Space group name H-M: P222

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Sample preparation

ComponentName: Human Aquaporin 2 from 2D electron diffraction data / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.028837 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
EM crystal formationInstrument: Dialysis machine / Lipid mixture: ecoli polar lipids / Lipid protein ratio: 0.4 / Temperature: 310 K / Time: 4 DAY
Buffer solutionpH: 6.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMMESC6H13NO4S1
2100 mMsodium chlorideNaCl1
35 mMmagnesium chlorideMgCl21
42.5 mMhistidineC6H9N3O21
52 percentoctyl glucosideC14H28O61
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Data collection

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: DIFFRACTION / Nominal defocus max: 0 nm / Nominal defocus min: 0 nm
Image recordingAverage exposure time: 1 sec. / Electron dose: 20 e/Å2 / Film or detector model: GATAN ULTRASCAN 1000 (2k x 2k) / Num. of diffraction images: 150 / Num. of grids imaged: 20 / Num. of real images: 100
Details: Electron micrographs were digitized with a Heidelberg Primescan D 7100 at 1 A/pixel at the specimen level. Diffraction patterns were recorded at 95 K, 200 kV, and a camera length of 1 m, ...Details: Electron micrographs were digitized with a Heidelberg Primescan D 7100 at 1 A/pixel at the specimen level. Diffraction patterns were recorded at 95 K, 200 kV, and a camera length of 1 m, using a Gatan UltraScanTM 2kx2k CCD camera
Image scansSampling size: 5.01 µm / Width: 4000 / Height: 4000
EM diffraction shellResolution: 2.6→66.96 Å / Fourier space coverage: 0.001 % / Multiplicity: 1 / Num. of structure factors: 53349 / Phase residual: 0.001 °
EM diffraction statsFourier space coverage: 70.98 % / High resolution: 2.6 Å / Num. of intensities measured: 53349 / Num. of structure factors: 53349 / Phase error rejection criteria: bayesan / Rmerge: 0.3097

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Processing

EM software
IDNameVersionCategory
3MRC IMAGE PROCESSING PACKAGECTF correction
8PHENIX3965molecular replacement
11IPLTcrystallography merging
19PHENIX3965model refinement
Image processingDetails: Images were processed using the MRC software package. Diffraction patterns were processed by the IPLT image processing library and toolkit (JSB 144, 4-12).
Crystal symmetry∠γ: 90 ° / C sampling length: 250 Å / A: 94.7 Å / B: 94.7 Å / C: 250 Å / Space group name H-M: P222
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.6 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 2D CRYSTAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross correlation coefficient
RefinementResolution: 2.6→66.963 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.97 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2956 2004 4.03 %
Rwork0.2934 --
obs0.2952 49751 70.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.0138323
ELECTRON CRYSTALLOGRAPHYf_angle_d1.98711248
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d16.7843156
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.0781271
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.0091366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.67040.22151010.27082539ELECTRON CRYSTALLOGRAPHY48
2.6704-2.7490.30231010.26082648ELECTRON CRYSTALLOGRAPHY50
2.749-2.83760.24171180.25492951ELECTRON CRYSTALLOGRAPHY56
2.8376-2.9390.26121420.27823524ELECTRON CRYSTALLOGRAPHY66
2.939-3.05660.28161460.27663747ELECTRON CRYSTALLOGRAPHY70
3.0566-3.19560.27961450.28443724ELECTRON CRYSTALLOGRAPHY70
3.1956-3.36390.30251570.28653896ELECTRON CRYSTALLOGRAPHY72
3.3639-3.57440.28851530.28793897ELECTRON CRYSTALLOGRAPHY73
3.5744-3.850.31471620.30174054ELECTRON CRYSTALLOGRAPHY75
3.85-4.23660.27341610.31774071ELECTRON CRYSTALLOGRAPHY76
4.2366-4.84790.32511630.30754168ELECTRON CRYSTALLOGRAPHY77
4.8479-6.10120.32191600.31674297ELECTRON CRYSTALLOGRAPHY78
6.1012-32.34390.33981670.30524339ELECTRON CRYSTALLOGRAPHY76

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