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- PDB-1sor: Aquaporin-0 membrane junctions reveal the structure of a closed w... -

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Basic information

Entry
Database: PDB / ID: 1sor
TitleAquaporin-0 membrane junctions reveal the structure of a closed water pore
ComponentsAquaporin-0
KeywordsMEMBRANE PROTEIN / membrane junction / water channel
Function / homology
Function and homology information


gap junction-mediated intercellular transport / water channel activity / water transport / structural constituent of eye lens / gap junction / response to stimulus / lens development in camera-type eye / positive regulation of cell adhesion / visual perception / protein homotetramerization ...gap junction-mediated intercellular transport / water channel activity / water transport / structural constituent of eye lens / gap junction / response to stimulus / lens development in camera-type eye / positive regulation of cell adhesion / visual perception / protein homotetramerization / calmodulin binding / endoplasmic reticulum / 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
Lens fiber major intrinsic protein
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / MOLECULAR REPLACEMENT / cryo EM / Resolution: 3 Å
AuthorsGonen, T. / Sliz, P. / Kistler, J. / Cheng, Y. / Walz, T.
CitationJournal: Nature / Year: 2004
Title: Aquaporin-0 membrane junctions reveal the structure of a closed water pore.
Authors: Tamir Gonen / Piotr Sliz / Joerg Kistler / Yifan Cheng / Thomas Walz /
Abstract: The lens-specific water pore aquaporin-0 (AQP0) is the only aquaporin known to form membrane junctions in vivo. We show here that AQP0 from the lens core, containing some carboxy-terminally cleaved ...The lens-specific water pore aquaporin-0 (AQP0) is the only aquaporin known to form membrane junctions in vivo. We show here that AQP0 from the lens core, containing some carboxy-terminally cleaved AQP0, forms double-layered crystals that recapitulate in vivo junctions. We present the structure of the AQP0 membrane junction as determined by electron crystallography. The junction is formed by three localized interactions between AQP0 molecules in adjoining membranes, mainly mediated by proline residues conserved in AQP0s from different species but not present in most other aquaporins. Whereas all previously determined aquaporin structures show the pore in an open conformation, the water pore is closed in AQP0 junctions. The water pathway in AQP0 also contains an additional pore constriction, not seen in other known aquaporin structures, which may be responsible for pore gating.
History
DepositionMar 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Data processing / Refinement description
Category: em_3d_reconstruction / em_image_scans / software
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Aug 23, 2023Group: 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
Remark 240EXPERIMENT TYPE : SINGLE-CRYSTAL ELECTRON DIFFRACTION DATE OF DATA COLLECTION : 28-JAN-2003 ...EXPERIMENT TYPE : SINGLE-CRYSTAL ELECTRON DIFFRACTION DATE OF DATA COLLECTION : 28-JAN-2003 TEMPERATURE (KELVIN) : 100.0 PH : 6.00 NUMBER OF CRYSTALS USED : 131 RADIATION SOURCE : ELECTRON MICROSCOPE X-RAY GENERATOR MODEL : TECNAI T20 OPTICS : CRYSTALS TILTED TO 0, 20, 45, 60 AND 70 DEGREES DETECTOR TYPE : CCD DETECTOR MANUFACTURER : GATAN 2K X 2K INTENSITY-INTEGRATION SOFTWARE : DIGITAL MICROGRAPH 3.7.4 DATA SCALING SOFTWARE : MRC NUMBER OF UNIQUE REFLECTIONS : 6635 RESOLUTION RANGE HIGH (A) : 3.000 RESOLUTION RANGE LOW (A) : 30.000 VERALL. COMPLETENESS FOR RANGE (%) : 88.0 DATA REDUNDANCY : 6.700 IN THE HIGHEST RESOLUTION SHELL. HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.50 COMPLETENESS FOR SHELL (%) : 82.0 DATA REDUNDANCY IN SHELL : 4.50 R MERGE FOR SHELL (I) : 0.54000 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT SOFTWARE USED: MOLREP 7.4.03 STARTING MODEL: PDB ENTRY 1J4N
Remark 999SEQUENCE The sequence of this protein has been deposited to gene bank. The accession number is AY573927.

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Structure visualization

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Assembly

Deposited unit
A: Aquaporin-0


Theoretical massNumber of molelcules
Total (without water)25,1731
Polymers25,1731
Non-polymers00
Water0
1
A: Aquaporin-0
x 8


Theoretical massNumber of molelcules
Total (without water)201,3888
Polymers201,3888
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area31700 Å2
ΔGint-323 kcal/mol
Surface area59330 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)65.500, 65.500, 160.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422

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Components

#1: Protein Aquaporin-0 / / MIP


Mass: 25173.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: Q6J8I9

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY / Number of used crystals: 131
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: aquaporin-0 / Type: COMPLEX
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
EM embeddingDetails: 10% glucose / Material: glucose
CrystalDensity Matthews: 3.45 Å3/Da / Density % sol: 64.04 %
Crystal growTemperature: 298 K / Method: microdialysis / pH: 6
Details: magnesium chloride, sodium chloride, MES, sodium azide, DTT, pH 6, MICRODIALYSIS, temperature 25K

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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: FLOOD BEAM
Electron lensMode: DIFFRACTION
Image recordingFilm or detector model: GENERIC GATAN (2k x 2k)
DiffractionMean temperature: 100 K
Diffraction sourceSource: ELECTRON MICROSCOPE / Type: Tecnai T20
DetectorType: Gatan 2K x 2K / Detector: CCD / Date: Jan 28, 2003 / Details: crystals tilted to 0, 20, 45, 60 and 70 degrees
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: electron
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 6635 / % possible obs: 88 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.16
Reflection shellResolution: 3→3.5 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.54 / % possible all: 82

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOLREPV. 7.4.03phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1J4N

1j4n


Resolution: 3→22.25 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 2281725.96 / Data cutoff high rms absF: 2281725.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.338 718 10.8 %RANDOM
Rwork0.299 ---
all0.307 6635 --
obs0.299 6635 88.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 74.19 Å2 / ksol: 0.330035 e/Å3
Displacement parametersBiso mean: 81.8 Å2
Baniso -1Baniso -2Baniso -3
1--13.27 Å20 Å20 Å2
2---13.27 Å20 Å2
3---26.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.51 Å
Luzzati d res low-5 Å
Luzzati sigma a0.71 Å0.7 Å
Refinement stepCycle: LAST / Resolution: 3→22.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 0 0 1778
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
ELECTRON CRYSTALLOGRAPHYc_bond_d0.005
ELECTRON CRYSTALLOGRAPHYc_angle_deg1
ELECTRON CRYSTALLOGRAPHYc_dihedral_angle_d17.4
ELECTRON CRYSTALLOGRAPHYc_improper_angle_d0.8
ELECTRON CRYSTALLOGRAPHYc_mcbond_it1.261.5
ELECTRON CRYSTALLOGRAPHYc_mcangle_it2.272
ELECTRON CRYSTALLOGRAPHYc_scbond_it1.162
ELECTRON CRYSTALLOGRAPHYc_scangle_it1.942.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.36 88 9.8 %
Rwork0.364 806 -
obs--74 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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