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- EMDB-3214: crystal structure of AQP4 bound to AZA -

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Basic information

Entry
Database: EMDB / ID: EMD-3214
Titlecrystal structure of AQP4 bound to AZA
Map dataReconstruction of rat aquaporin-4 bound to acetazolamide
Sample
  • Sample: Aquaporin-4 bound to acetazolamide
  • Protein or peptide: aquaporin-4
Keywordswater channel / aquaporin
Function / homology
Function and homology information


Passive transport by Aquaporins / cerebrospinal fluid secretion / renal water absorption / regulation of vascular endothelial growth factor production / cerebrospinal fluid circulation / astrocyte end-foot / intracellular water homeostasis / water channel activity / water transport / negative regulation of cell adhesion molecule production ...Passive transport by Aquaporins / cerebrospinal fluid secretion / renal water absorption / regulation of vascular endothelial growth factor production / cerebrospinal fluid circulation / astrocyte end-foot / intracellular water homeostasis / water channel activity / water transport / negative regulation of cell adhesion molecule production / cell projection membrane / multicellular organismal-level water homeostasis / cellular response to interleukin-6 / Vasopressin regulates renal water homeostasis via Aquaporins / negative regulation of interleukin-1 beta production / negative regulation of interleukin-6 production / cellular response to interleukin-1 / response to glucocorticoid / T-tubule / basal plasma membrane / cellular response to estradiol stimulus / female pregnancy / establishment of localization in cell / cellular response to glucose stimulus / sensory perception of sound / carbon dioxide transport / sarcolemma / cellular response to type II interferon / cell-cell adhesion / cell-cell junction / basolateral plasma membrane / protein homotetramerization / endosome membrane / external side of plasma membrane / protein-containing complex / extracellular region / identical protein binding / plasma membrane / cytoplasm
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 speciesRattus norvegicus (Norway rat)
Methodelectron crystallography / cryo EM / Resolution: 5.0 Å
AuthorsKamegawa A / Hiroaki Y / Tani K / Fujiyoshi Y
CitationJournal: Microscopy (Oxf) / Year: 2016
Title: Two-dimensional crystal structure of aquaporin-4 bound to the inhibitor acetazolamide.
Authors: Akiko Kamegawa / Yoko Hiroaki / Kazutoshi Tani / Yoshinori Fujiyoshi /
Abstract: Acetazolamide (AZA) reduces the water permeability of aquaporin-4, the predominant water channel in the brain. We determined the structure of aquaporin-4 in the presence of AZA using electron ...Acetazolamide (AZA) reduces the water permeability of aquaporin-4, the predominant water channel in the brain. We determined the structure of aquaporin-4 in the presence of AZA using electron crystallography. Most of the features of the 5-Å density map were consistent with those of the previously determined atomic model. The map showed a protruding density from near the extracellular pore entrance, which most likely represents the bound AZA. Molecular docking simulations supported the location of the protrusion as the likely AZA-binding site. These findings suggest that AZA reduces water conduction by obstructing the pathway at the extracellular entrance without inducing a large conformational change in the protein.
History
DepositionOct 26, 2015-
Header (metadata) releaseNov 4, 2015-
Map releaseDec 30, 2015-
UpdateApr 13, 2016-
Current statusApr 13, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.11
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.11
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3214_tet...

Downloads & links

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Map

FileDownload / File: emd_3214.map.gz / Format: CCP4 / Size: 1.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of rat aquaporin-4 bound to acetazolamide
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.25 Å/pix.
x 129 pix.
= 161.25 Å		1.15 Å/pix.
x 61 pix.
= 70.272 Å		1.15 Å/pix.
x 61 pix.
= 70.272 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX: 1.152 Å / Y: 1.152 Å / Z: 1.25 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.11 / Movie #1: 1.11
Minimum - Maximum-4.95270014 - 4.44810009
Average (Standard dev.)-0.00934387 (±0.99871641)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-300-64
Dimensions6161129
Spacing6161129
CellA: 70.271996 Å / B: 70.271996 Å / C: 161.25 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1521.1521.25
M x/y/z6161129
origin x/y/z0.0000.0000.000
length x/y/z70.27270.272161.250
α/β/γ90.00090.00090.000
start NX/NY/NZ-300-64
NX/NY/NZ6161129
MAP C/R/S213
start NC/NR/NS0-30-64
NC/NR/NS6161129
D min/max/mean-4.9534.448-0.009

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Supplemental data

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Sample components

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Entire : Aquaporin-4 bound to acetazolamide

EntireName: Aquaporin-4 bound to acetazolamide
Components
  • Sample: Aquaporin-4 bound to acetazolamide
  • Protein or peptide: aquaporin-4

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Supramolecule #1000: Aquaporin-4 bound to acetazolamide

SupramoleculeName: Aquaporin-4 bound to acetazolamide / type: sample / ID: 1000 / Details: The sample was 2D crystal / Oligomeric state: two tetramers of AQP4 in unit cell / Number unique components: 1

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Macromolecule #1: aquaporin-4

MacromoleculeName: aquaporin-4 / type: protein_or_peptide / ID: 1 / Name.synonym: AQP4 / Oligomeric state: tetramer / Recombinant expression: Yes
Source (natural)Organism: Rattus norvegicus (Norway rat) / synonym: Rat / Location in cell: Plasma membrane
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceUniProtKB: Aquaporin-4 / GO: water transport / InterPro: INTERPRO: IPR012269

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron crystallography
Aggregation state2D array

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Sample preparation

BufferpH: 6
Details: 10 mM MES, 100 mM NaCl, 50 mM MgCl2, 2 mM dithiothreitol, and 1% glycerol
GridDetails: molybdenum grid with thin carbon support
VitrificationCryogen name: NITROGEN / Instrument: LEICA KF80
DetailsCrystals grown in dialysis
Crystal formationDetails: Crystals grown in dialysis

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Electron microscopy

MicroscopeJEOL KYOTO-3000SFF
TemperatureMin: 4 K / Average: 4 K
DateJun 10, 2009
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 141 / Average electron dose: 20 e/Å2 / Bits/pixel: 14
Tilt angle min0
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.6 mm / Nominal defocus max: 4.34 µm / Nominal defocus min: 0.52 µm / Nominal magnification: 40000
Sample stageSpecimen holder: Helium cooled / Specimen holder model: JEOL / Tilt angle max: 60 / Tilt series - Axis1 - Min angle: 0 ° / Tilt series - Axis1 - Max angle: 60 °

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Image processing

DetailsImages were processed using a modified MRC suite.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Software - Name: MRC
Crystal parametersUnit cell - A: 69.1 Å / Unit cell - B: 69.1 Å / Unit cell - C: 160.0 Å / Unit cell - γ: 90.0 ° / Unit cell - α: 90.0 ° / Unit cell - β: 90.0 ° / Plane group: P 4 21 2
CTF correctionDetails: Each micrograph

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