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Yorodumi- PDB-6pv6: Functional Pathways of Biomolecules Retrieved from Single-particl... -
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-Basic information
Entry | Database: PDB / ID: 6pv6 | ||||||
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Title | Functional Pathways of Biomolecules Retrieved from Single-particle Snapshots | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / ion channel / Ca2+ channel / excitation/contraction coupling | ||||||
Function / homology | Function and homology information positive regulation of sequestering of calcium ion / cyclic nucleotide binding / negative regulation of release of sequestered calcium ion into cytosol / negative regulation of insulin secretion involved in cellular response to glucose stimulus / neuronal action potential propagation / insulin secretion involved in cellular response to glucose stimulus / cell communication by electrical coupling involved in cardiac conduction / 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 release of sequestered calcium ion into cytosol / negative regulation of insulin secretion involved in cellular response to glucose stimulus / neuronal action potential propagation / insulin secretion involved in cellular response to glucose stimulus / cell communication by electrical coupling involved in cardiac conduction / response to redox state / protein maturation by protein folding / 'de novo' protein folding / negative regulation of heart rate / negative regulation of phosphoprotein phosphatase activity / FK506 binding / positive regulation of axon regeneration / : / smooth muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / response to vitamin E / calcium channel inhibitor activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / protein peptidyl-prolyl isomerization / T cell proliferation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / release of sequestered calcium ion into cytosol / regulation of ryanodine-sensitive calcium-release channel activity / Ion homeostasis / sarcoplasmic reticulum membrane / calcium channel complex / regulation of cytosolic calcium ion concentration / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / 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) Oryctolagus cuniculus (rabbit) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å | ||||||
Authors | Dashti, A. / des Georges, A. / Frank, J. / Ourmazd, A. | ||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Retrieving functional pathways of biomolecules from single-particle snapshots. Authors: Ali Dashti / Ghoncheh Mashayekhi / Mrinal Shekhar / Danya Ben Hail / Salah Salah / Peter Schwander / Amedee des Georges / Abhishek Singharoy / Joachim Frank / Abbas Ourmazd / Abstract: A primary reason for the intense interest in structural biology is the fact that knowledge of structure can elucidate macromolecular functions in living organisms. Sustained effort has resulted in an ...A primary reason for the intense interest in structural biology is the fact that knowledge of structure can elucidate macromolecular functions in living organisms. Sustained effort has resulted in an impressive arsenal of tools for determining the static structures. But under physiological conditions, macromolecules undergo continuous conformational changes, a subset of which are functionally important. Techniques for capturing the continuous conformational changes underlying function are essential for further progress. Here, we present chemically-detailed conformational movies of biological function, extracted data-analytically from experimental single-particle cryo-electron microscopy (cryo-EM) snapshots of ryanodine receptor type 1 (RyR1), a calcium-activated calcium channel engaged in the binding of ligands. The functional motions differ substantially from those inferred from static structures in the nature of conformationally active structural domains, the sequence and extent of conformational motions, and the way allosteric signals are transduced within and between domains. Our approach highlights the importance of combining experiment, advanced data analysis, and molecular simulations. #1: Journal: NAT COMMUN / Year: 2020 Title: Functional Pathways of Biomolecules Retrieved from Single-particle Snapshots Authors: Dashti, A. / des Georges, A. / Frank, J. / Ourmazd, A. | ||||||
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 | 6pv6.cif.gz | 2.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6pv6.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6pv6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/6pv6 ftp://data.pdbj.org/pub/pdb/validation_reports/pv/6pv6 | HTTPS FTP |
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-Related structure data
Related structure data | 20486MC 7jmfC 7jmgC 7jmhC 7jmiC 7jmjC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10315 (Title: Cryo electron microscopy of RyR1 in the presence and abscence of Ca, Caffeine and ATP ligands Data size: 334.2 Data #1: Aligned stacks of images for both -/+ Ligand RyR1 datasets [picked particles - single frame - processed]) |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 502246.719 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: thigh #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 #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-CA / Has ligand of interest | Y | Sequence details | The full sequence for the bigger protein of chains B,E,I,G is the following: ...The full sequence for the bigger protein of chains B,E,I,G is the following: MGDGGEGEDE | |
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