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Yorodumi- PDB-7lhe: Structure of full-length IP3R1 channel reconstituted into lipid n... -
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-Basic information
Entry | Database: PDB / ID: 7lhe | ||||||||||||||||||||||||
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Title | Structure of full-length IP3R1 channel reconstituted into lipid nanodisc in the apo-state | ||||||||||||||||||||||||
Components | Inositol 1,4,5-trisphosphate receptor type 1 | ||||||||||||||||||||||||
Keywords | MEMBRANE PROTEIN / Calcium channel / lipid nanodisc | ||||||||||||||||||||||||
Function / homology | Function and homology information Effects of PIP2 hydrolysis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / inositol 1,4,5-trisphosphate receptor activity involved in regulation of postsynaptic cytosolic calcium levels / release of sequestered calcium ion into cytosol by endoplasmic reticulum / Elevation of cytosolic Ca2+ levels / cGMP effects / smooth endoplasmic reticulum membrane / platelet dense tubular network / calcineurin complex / platelet dense granule membrane ...Effects of PIP2 hydrolysis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / inositol 1,4,5-trisphosphate receptor activity involved in regulation of postsynaptic cytosolic calcium levels / release of sequestered calcium ion into cytosol by endoplasmic reticulum / Elevation of cytosolic Ca2+ levels / cGMP effects / smooth endoplasmic reticulum membrane / platelet dense tubular network / calcineurin complex / platelet dense granule membrane / epithelial fluid transport / ion channel modulating, G protein-coupled receptor signaling pathway / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / inositol 1,4,5-trisphosphate-gated calcium channel activity / calcium import into the mitochondrion / regulation of postsynaptic cytosolic calcium ion concentration / voluntary musculoskeletal movement / inositol 1,4,5 trisphosphate binding / positive regulation of calcium ion transport / negative regulation of calcium-mediated signaling / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / endoplasmic reticulum calcium ion homeostasis / positive regulation of hepatocyte proliferation / nuclear inner membrane / transport vesicle membrane / Ion homeostasis / dendrite development / intracellularly gated calcium channel activity / ligand-gated ion channel signaling pathway / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / single fertilization / GABA-ergic synapse / calcium channel inhibitor activity / cellular response to cAMP / release of sequestered calcium ion into cytosol / regulation of cytosolic calcium ion concentration / liver regeneration / phosphatidylinositol binding / secretory granule membrane / post-embryonic development / sarcoplasmic reticulum / synaptic membrane / calcium ion transmembrane transport / calcium-mediated signaling / cell morphogenesis / positive regulation of insulin secretion / Schaffer collateral - CA1 synapse / positive regulation of neuron projection development / nuclear envelope / calcium ion transport / presynapse / cellular response to hypoxia / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / protein phosphatase binding / protein homotetramerization / transmembrane transporter binding / postsynapse / postsynaptic density / response to hypoxia / protein domain specific binding / positive regulation of apoptotic process / neuronal cell body / synapse / dendrite / calcium ion binding / endoplasmic reticulum membrane / negative regulation of apoptotic process / protein-containing complex binding / nucleolus / perinuclear region of cytoplasm / endoplasmic reticulum / protein-containing complex / ATP binding / identical protein binding / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||||||||||||||||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||||||||||||||
Authors | Baker, M.R. / Fan, G. / Baker, M.L. / Serysheva, I.I. | ||||||||||||||||||||||||
Funding support | United States, 7items
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Citation | Journal: Commun Biol / Year: 2021 Title: Cryo-EM structure of type 1 IPR channel in a lipid bilayer. Authors: Mariah R Baker / Guizhen Fan / Alexander B Seryshev / Melina A Agosto / Matthew L Baker / Irina I Serysheva / Abstract: Type 1 inositol 1,4,5-trisphosphate receptor (IPR1) is the predominant Ca-release channel in neurons. IPR1 mediates Ca release from the endoplasmic reticulum into the cytosol and thereby is involved ...Type 1 inositol 1,4,5-trisphosphate receptor (IPR1) is the predominant Ca-release channel in neurons. IPR1 mediates Ca release from the endoplasmic reticulum into the cytosol and thereby is involved in many physiological processes. Here, we present the cryo-EM structures of full-length rat IPR1 reconstituted in lipid nanodisc and detergent solubilized in the presence of phosphatidylcholine determined in ligand-free, closed states by single-particle electron cryo-microscopy. Notably, both structures exhibit the well-established IPR1 protein fold and reveal a nearly complete representation of lipids with similar locations of ordered lipids bound to the transmembrane domains. The lipid-bound structures show improved features that enabled us to unambiguously build atomic models of IPR1 including two membrane associated helices that were not previously resolved in the TM region. Our findings suggest conserved locations of protein-bound lipids among homotetrameric ion channels that are critical for their structural and functional integrity despite the diversity of structural mechanisms for their gating. | ||||||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7lhe.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7lhe.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 7lhe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lhe_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 7lhe_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 7lhe_validation.xml.gz | 242.7 KB | Display | |
Data in CIF | 7lhe_validation.cif.gz | 359 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lh/7lhe ftp://data.pdbj.org/pub/pdb/validation_reports/lh/7lhe | HTTPS FTP |
-Related structure data
Related structure data | 23337MC 7lhfC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 311848.250 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Organ: cerebellum / References: UniProt: P29994 #2: Chemical | ChemComp-PLX / ( #3: Chemical | ChemComp-ZN / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Type 1 inositol 1,4,5-trisphosphate receptor tetrameric protein complex Type: COMPLEX / Entity ID: #1 / Source: NATURAL |
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Molecular weight | Value: 1.3 MDa / Experimental value: NO |
Source (natural) | Organism: Rattus norvegicus (Norway rat) / Cellular location: membrane / Organ: cerebellum / Organelle: endoplasmic reticulum |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Calibrated magnification: 46943 X / Nominal defocus max: 3500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 0.2 sec. / Electron dose: 56 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of real images: 22000 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Sampling size: 5 µm / Width: 3840 / Height: 3712 / Movie frames/image: 35 / Used frames/image: 2-35 |
-Processing
Software | Name: PHENIX / Version: dev_svn: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 573723 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6MU2 Accession code: 6MU2 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||
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