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- EMDB-5278: 3D structure of a full-length type 1 inositol 1,4,5-trisphosphate... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-5278 | |||||||||
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Title | 3D structure of a full-length type 1 inositol 1,4,5-trisphosphate receptor in the closed state | |||||||||
![]() | This is a Cryo-EM density map of IP3R1 in the closed state. | |||||||||
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![]() | type 1 inositol 1 / 4 / 5-trisphosphate receptor / calcium channel / closed state / single particle cryo-EM | |||||||||
Function / homology | RIH domain / endoplasmic reticulum membrane![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 9.5 Å | |||||||||
![]() | Ludtke SJ / Tran TP / Ngo QT / Moiseenkova-Bell VY / Chiu W / Serysheva II | |||||||||
![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 56.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.7 KB 10.7 KB | Display Display | ![]() |
Images | ![]() | 1.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 79.3 KB | Display | ![]() |
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Full document | ![]() | 78.4 KB | Display | |
Data in XML | ![]() | 494 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is a Cryo-EM density map of IP3R1 in the closed state. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.81 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Type 1 Inositol 1,4,5-Trisphosphate Receptor
Entire | Name: Type 1 Inositol 1,4,5-Trisphosphate Receptor |
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Components |
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-Supramolecule #1000: Type 1 Inositol 1,4,5-Trisphosphate Receptor
Supramolecule | Name: 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 |
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Molecular weight | Theoretical: 1.3 MDa |
-Macromolecule #1: Ion channel
Macromolecule | Name: 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 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 1.3 MDa |
Sequence | GO: endoplasmic reticulum membrane / InterPro: RIH domain |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.4 Details: 50 mM Tris-HCl, 150 mM sodium chloride, 1 mM DTT, 1 mM EDTA, 0.4% CHAPS, 5% sucrose, protease inhibitors |
Staining | Type: NEGATIVE / Details: Frozen-hydrated |
Grid | Details: 400 mesh Quantifoil holey grids covered with a continuous carbon film |
Vitrification | Cryogen 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
Microscope | JEOL 2010F |
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Temperature | Min: 103 K / Max: 104 K / Average: 103 K |
Image recording | Category: 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 beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination 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 stage | Specimen holder: Side entry liquid nitrogen-cooled / Specimen holder model: GATAN LIQUID NITROGEN |
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Image processing
Details | 869 CCD frames |
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CTF correction | Details: Per particle phase-flipping with amplitude correction of class-averages |
Final reconstruction | Algorithm: 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 |