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Yorodumi- PDB-8eaq: Structure of the full-length IP3R1 channel determined at high Ca2+ -
+Open data
-Basic information
Entry | Database: PDB / ID: 8eaq | ||||||||||||||||||||||||
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Title | Structure of the full-length IP3R1 channel determined at high Ca2+ | ||||||||||||||||||||||||
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: 3.26 Å | ||||||||||||||||||||||||
Authors | Fan, G. / Baker, M.R. / Terry, L.E. / Arige, V. / Chen, M. / Seryshev, A.B. / Baker, M.L. / Ludtke, S.J. / Yule, D.I. / Serysheva, I.I. | ||||||||||||||||||||||||
Funding support | United States, 7items
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Citation | Journal: Nat Commun / Year: 2022 Title: Conformational motions and ligand-binding underlying gating and regulation in IPR channel. Authors: Guizhen Fan / Mariah R Baker / Lara E Terry / Vikas Arige / Muyuan Chen / Alexander B Seryshev / Matthew L Baker / Steven J Ludtke / David I Yule / Irina I Serysheva / Abstract: Inositol-1,4,5-trisphosphate receptors (IPRs) are activated by IP and Ca and their gating is regulated by various intracellular messengers that finely tune the channel activity. Here, using single ...Inositol-1,4,5-trisphosphate receptors (IPRs) are activated by IP and Ca and their gating is regulated by various intracellular messengers that finely tune the channel activity. Here, using single particle cryo-EM analysis we determined 3D structures of the nanodisc-reconstituted IPR1 channel in two ligand-bound states. These structures provide unprecedented details governing binding of IP, Ca and ATP, revealing conformational changes that couple ligand-binding to channel opening. Using a deep-learning approach and 3D variability analysis we extracted molecular motions of the key protein domains from cryo-EM density data. We find that IP binding relies upon intrinsic flexibility of the ARM2 domain in the tetrameric channel. Our results highlight a key role of dynamic side chains in regulating gating behavior of IPR channels. This work represents a stepping-stone to developing mechanistic understanding of conformational pathways underlying ligand-binding, activation and regulation of the channel. | ||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8eaq.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8eaq.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8eaq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8eaq_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 8eaq_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 8eaq_validation.xml.gz | 255.3 KB | Display | |
Data in CIF | 8eaq_validation.cif.gz | 375.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ea/8eaq ftp://data.pdbj.org/pub/pdb/validation_reports/ea/8eaq | HTTPS FTP |
-Related structure data
Related structure data | 27982MC 8earC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 313657.406 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-ZN / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-PLX / ( 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 | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: reconstituted in lipid nanodisc |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 |
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: 2500 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: 49 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of real images: 25125 |
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 |
-Processing
Software |
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1955320 / Details: NeuralNet autopicking in EMAN2 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 346731 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7LHE | ||||||||||||||||||||||||||||||||||||||||
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