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- EMDB-5278: 3D structure of a full-length type 1 inositol 1,4,5-trisphosphate... -

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Basic information

Entry
Database: EMDB / ID: EMD-5278
Title3D structure of a full-length type 1 inositol 1,4,5-trisphosphate receptor in the closed state
Map dataThis is a Cryo-EM density map of IP3R1 in the closed state.
Sample
  • Sample: Type 1 Inositol 1,4,5-Trisphosphate Receptor
  • Protein or peptide: Ion channel
Keywordstype 1 inositol 1 / 4 / 5-trisphosphate receptor / calcium channel / closed state / single particle cryo-EM
Function / homologyRIH domain / endoplasmic reticulum membrane
Function and homology information
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 9.5 Å
AuthorsLudtke SJ / Tran TP / Ngo QT / Moiseenkova-Bell VY / Chiu W / Serysheva II
CitationJournal: Structure / Year: 2011
Title: Flexible architecture of IP3R1 by Cryo-EM.
Authors: Steven J Ludtke / Thao P Tran / Que T Ngo / Vera Yu Moiseenkova-Bell / Wah Chiu / Irina I Serysheva /
Abstract: Inositol 1,4,5-trisphosphate receptors (IP3Rs) play a fundamental role in generating Ca2+ signals that trigger many cellular processes in virtually all eukaryotic cells. Thus far, the three- ...Inositol 1,4,5-trisphosphate receptors (IP3Rs) play a fundamental role in generating Ca2+ signals that trigger many cellular processes in virtually all eukaryotic cells. Thus far, the three-dimensional (3D) structure of these channels has remained extremely controversial. Here, we report a subnanometer resolution electron cryomicroscopy (cryo-EM) structure of a fully functional type 1 IP3R from cerebellum in the closed state. The transmembrane region reveals a twisted bundle of four α helices, one from each subunit, that form a funnel shaped structure around the 4-fold symmetry axis, strikingly similar to the ion-conduction pore of K+ channels. The lumenal face of IP3R1 has prominent densities that surround the pore entrance and similar to the highly structured turrets of Kir channels. 3D statistical analysis of the cryo-EM density map identifies high variance in the cytoplasmic region. This structural variation could be attributed to genuine structural flexibility of IP3R1.
History
DepositionApr 26, 2011-
Header (metadata) releaseMay 9, 2011-
Map releaseAug 9, 2011-
UpdateSep 12, 2011-
Current statusSep 12, 2011Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5278.png

Downloads & links

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Map

FileDownload / File: emd_5278.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a Cryo-EM density map of IP3R1 in the closed state.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.81 Å/pix.
x 256 pix.
= 463.36 Å		1.81 Å/pix.
x 256 pix.
= 463.36 Å		1.81 Å/pix.
x 256 pix.
= 463.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-0.675821 - 3.15368
Average (Standard dev.)0.043066 (±0.198278)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 463.36 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.811.811.81
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z463.360463.360463.360
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-0.6763.1540.043

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Supplemental data

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Sample components

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Entire : Type 1 Inositol 1,4,5-Trisphosphate Receptor

EntireName: Type 1 Inositol 1,4,5-Trisphosphate Receptor
Components
  • Sample: Type 1 Inositol 1,4,5-Trisphosphate Receptor
  • Protein or peptide: Ion channel

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Supramolecule #1000: Type 1 Inositol 1,4,5-Trisphosphate Receptor

SupramoleculeName: Type 1 Inositol 1,4,5-Trisphosphate Receptor / type: sample / ID: 1000
Details: The sample was frozen immediately upon channel protein purification
Oligomeric state: Tetramer / Number unique components: 1
Molecular weightTheoretical: 1.3 MDa

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Macromolecule #1: Ion channel

MacromoleculeName: Ion channel / type: protein_or_peptide / ID: 1 / Name.synonym: IP3R1
Details: IP3R1 channel was solubilized with CHAPS from rat cerebellum and purified by immunoaffinity chromatography.
Number of copies: 4 / Oligomeric state: Tetramer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Rattus norvegicus (Norway rat) / synonym: Rat / Tissue: Cerebellum / Organelle: Endoplasmic Reticulum Membranes / Location in cell: Integral membrane protein
Molecular weightTheoretical: 1.3 MDa
SequenceGO: endoplasmic reticulum membrane / InterPro: RIH domain

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.4
Details: 50 mM Tris-HCl, 150 mM sodium chloride, 1 mM DTT, 1 mM EDTA, 0.4% CHAPS, 5% sucrose, protease inhibitors
StainingType: NEGATIVE / Details: Frozen-hydrated
GridDetails: 400 mesh Quantifoil holey grids covered with a continuous carbon film
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 101 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot (FEI) / Method: Blot for 2-3 sec before plunging

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Electron microscopy

MicroscopeJEOL 2010F
TemperatureMin: 103 K / Max: 104 K / Average: 103 K
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN (4k x 4k) / Digitization - Sampling interval: 1.81 µm / Number real images: 869 / Average electron dose: 18 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.4 µm / Nominal magnification: 60000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

Details869 CCD frames
CTF correctionDetails: Per particle phase-flipping with amplitude correction of class-averages
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN1.9
Details: Direct Fourier Inversion based on Wiener-filtered and CTF amplitude-corrected class-averages
Number images used: 37231

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