+Open data
-Basic information
Entry | Database: PDB / ID: 6ji0 | ||||||
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Title | Structure of RyR2 (F/A/C/Ca2+ dataset) | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / cryo-EM | ||||||
Function / homology | Function and homology information positive regulation of sequestering of calcium ion / cyclic nucleotide binding / negative regulation of calcium-mediated signaling / negative regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of release of sequestered calcium ion into cytosol / neuronal action potential propagation / insulin secretion involved in cellular response to glucose stimulus / response to redox state / protein maturation by protein folding / 'de novo' protein folding ...positive regulation of sequestering of calcium ion / cyclic nucleotide binding / negative regulation of calcium-mediated signaling / negative regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of release of sequestered calcium ion into cytosol / neuronal action potential propagation / insulin secretion involved in cellular response to glucose stimulus / response to redox state / protein maturation by protein folding / 'de novo' protein folding / negative regulation of heart rate / FK506 binding / positive regulation of axon regeneration / channel regulator activity / smooth muscle contraction / response to vitamin E / calcium channel inhibitor activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / T cell proliferation / Ion homeostasis / release of sequestered calcium ion into cytosol / regulation of cytosolic calcium ion concentration / sarcoplasmic reticulum membrane / calcium channel complex / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / calcium-mediated signaling / response to hydrogen peroxide / Stimuli-sensing channels / Z disc / positive regulation of cytosolic calcium ion concentration / protein refolding / transmembrane transporter binding / signaling receptor binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Sus scrofa (pig) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å | ||||||
Authors | Gong, D.S. / Chi, X.M. / Zhou, G.W. / Huang, G.X.Y. / Lei, J.L. / Yan, N. | ||||||
Citation | Journal: Nature / Year: 2019 Title: Modulation of cardiac ryanodine receptor 2 by calmodulin. Authors: Deshun Gong / Ximin Chi / Jinhong Wei / Gewei Zhou / Gaoxingyu Huang / Lin Zhang / Ruiwu Wang / Jianlin Lei / S R Wayne Chen / Nieng Yan / Abstract: The high-conductance intracellular calcium (Ca) channel RyR2 is essential for the coupling of excitation and contraction in cardiac muscle. Among various modulators, calmodulin (CaM) regulates RyR2 ...The high-conductance intracellular calcium (Ca) channel RyR2 is essential for the coupling of excitation and contraction in cardiac muscle. Among various modulators, calmodulin (CaM) regulates RyR2 in a Ca-dependent manner. Here we reveal the regulatory mechanism by which porcine RyR2 is modulated by human CaM through the structural determination of RyR2 under eight conditions. Apo-CaM and Ca-CaM bind to distinct but overlapping sites in an elongated cleft formed by the handle, helical and central domains. The shift in CaM-binding sites on RyR2 is controlled by Ca binding to CaM, rather than to RyR2. Ca-CaM induces rotations and intradomain shifts of individual central domains, resulting in pore closure of the PCB95 and Ca-activated channel. By contrast, the pore of the ATP, caffeine and Ca-activated channel remains open in the presence of Ca-CaM, which suggests that Ca-CaM is one of the many competing modulators of RyR2 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 | 6ji0.cif.gz | 2.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6ji0.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6ji0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ji0_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6ji0_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6ji0_validation.xml.gz | 347.6 KB | Display | |
Data in CIF | 6ji0_validation.cif.gz | 538.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/6ji0 ftp://data.pdbj.org/pub/pdb/validation_reports/ji/6ji0 | HTTPS FTP |
-Related structure data
Related structure data | 9831MC 9833C 9834C 9836C 9837C 9879C 9880C 9889C 6ji8C 6jiiC 6jiuC 6jiyC 6jrrC 6jrsC 6jv2C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10241 (Title: afTMEM16/nanodisc complex in the absence of Ca2+ / Data size: 162.0 Data #1: motion corrected 2D micrographs from 45 frames of afTMEM16/nanodisc complex in the absence of Ca2+ [micrographs - single frame]) |
-Links
-Assembly
Deposited unit |
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-Components
-Protein , 2 types, 8 molecules ACEGBDFH
#1: Protein | Mass: 564905.625 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) #2: Protein | Mass: 11798.501 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP1B, FKBP12.6, FKBP1L, FKBP9, OTK4 / Production host: Escherichia coli (E. coli) / References: UniProt: P68106, peptidylprolyl isomerase |
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-Non-polymers , 4 types, 16 molecules
#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-ATP / #5: Chemical | ChemComp-CA / #6: Chemical | ChemComp-CFF / |
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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: RyR2 in complex with FKBP12.6 / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL |
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Source (natural) | Organism: Sus scrofa (pig) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||||||
3D reconstruction | Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 78841 / Symmetry type: POINT |