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- EMDB-1061: Inositol 1,4,5-trisphosphate receptor contains multiple cavities ... -

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Basic information

Entry
Database: EMDB / ID: EMD-1061
TitleInositol 1,4,5-trisphosphate receptor contains multiple cavities and L-shaped ligand-binding domains.
Map data3D volume data
Sample
  • Sample: IP3 receptor from mouse
  • Protein or peptide: IP3 receptor
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 15.0 Å
AuthorsSato C / Hamada K / Ogura T / Miyazawa A / Iwasaki K / Hiroaki Y / Tani K / Terauchi A / Fujiyoshi Y / Mikoshiba K
CitationJournal: J Mol Biol / Year: 2004
Title: Inositol 1,4,5-trisphosphate receptor contains multiple cavities and L-shaped ligand-binding domains.
Authors: Chikara Sato / Kozo Hamada / Toshihiko Ogura / Atsuo Miyazawa / Kenji Iwasaki / Yoko Hiroaki / Kazutoshi Tani / Akiko Terauchi / Yoshinori Fujiyoshi / Katsuhiko Mikoshiba /
Abstract: Calcium concentrations are strictly regulated in all biological cells, and one of the key molecules responsible for this regulation is the inositol 1,4,5-trisphosphate receptor, which was known to ...Calcium concentrations are strictly regulated in all biological cells, and one of the key molecules responsible for this regulation is the inositol 1,4,5-trisphosphate receptor, which was known to form a homotetrameric Ca(2+) channel in the endoplasmic reticulum. The receptor is involved in neuronal transmission via Ca(2+) signaling and for many other functions that relate to morphological and physiological processes in living organisms. We analysed the three-dimensional structure of the ligand-free form of the receptor based on a single-particle technique using an originally developed electron microscope equipped with a helium-cooled specimen stage and an automatic particle picking system. We propose a model that explains the complex mechanism for the regulation of Ca(2+) release by co-agonists, Ca(2+), inositol 1,4,5-trisphosphate based on the structure of multiple internal cavities and a porous balloon-shaped cytoplasmic domain containing a prominent L-shaped density which was assigned by the X-ray structure of the inositol 1,4,5-trisphosphate binding domain.
History
DepositionNov 25, 2003-
Header (metadata) releaseDec 16, 2003-
Map releaseDec 16, 2005-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1061.gif

Downloads & links

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Map

FileDownload / File: emd_1061.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D volume data
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.6 Å/pix.
x 100 pix.
= 260. Å		2.6 Å/pix.
x 100 pix.
= 260. Å		2.6 Å/pix.
x 100 pix.
= 260. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.6 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.0637 / Movie #1: 0.012
Minimum - Maximum-0.290988 - 0.493128
Average (Standard dev.)0.000154374 (±0.0408507)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 260 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.62.62.6
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z260.000260.000260.000
α/β/γ90.00090.00090.000
start NX/NY/NZ0052
NX/NY/NZ12812855
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-0.2910.4930.000

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Supplemental data

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Sample components

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Entire : IP3 receptor from mouse

EntireName: IP3 receptor from mouse
Components
  • Sample: IP3 receptor from mouse
  • Protein or peptide: IP3 receptor

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Supramolecule #1000: IP3 receptor from mouse

SupramoleculeName: IP3 receptor from mouse / type: sample / ID: 1000 / Oligomeric state: tetramer / Number unique components: 1
Molecular weightTheoretical: 1.3 MDa

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Macromolecule #1: IP3 receptor

MacromoleculeName: IP3 receptor / type: protein_or_peptide / ID: 1 / Name.synonym: IP3R / Details: in 1mM EGTA / Number of copies: 4 / Oligomeric state: tetramer / Recombinant expression: Yes
Source (natural)Organism: Mus musculus (house mouse) / Strain: IP3R1 / synonym: mouse / Tissue: cerebella / Organelle: microsomal membrane / Location in cell: endoplasmic reticulum
Molecular weightExperimental: 1.3 MDa
Recombinant expressionOrganism: natural source (unknown)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL KYOTO-3000SFF
TemperatureAverage: 4.2 K
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: top entry / Specimen holder model: OTHER

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Image processing

Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 3 SIGMA CUT-OFF

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