[English] 日本語
Yorodumi- PDB-7jmh: Functional Pathways of Biomolecules Retrieved from Single-particl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jmh | |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Functional Pathways of Biomolecules Retrieved from Single-particle Snapshots - Frame 35 - State 4 (S4) | |||||||||||||||||||||||||||
Components |
| |||||||||||||||||||||||||||
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 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 / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / T cell proliferation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / release of sequestered calcium ion into cytosol / regulation of cytosolic calcium ion concentration / calcium channel complex / sarcoplasmic reticulum membrane / 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) 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. | |||||||||||||||||||||||||||
Funding support | United States, 8items
| |||||||||||||||||||||||||||
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. / Singharoy, A. / Frank, J. / Ourmazd, A. | |||||||||||||||||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7jmh.cif.gz | 2.8 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7jmh.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7jmh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jmh_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7jmh_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7jmh_validation.xml.gz | 372.3 KB | Display | |
Data in CIF | 7jmh_validation.cif.gz | 592.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jm/7jmh ftp://data.pdbj.org/pub/pdb/validation_reports/jm/7jmh | HTTPS FTP |
-Related structure data
Related structure data | 22394MC 6pv6C 7jmfC 7jmgC 7jmiC 7jmjC C: citing same article (ref.) M: map data used to model this data |
---|---|
Similar structure data | |
Experimental dataset #1 | Data reference: 10.6019/EMPIAR-10315 / Data set type: EMPIAR / Metadata reference: 10.6019/EMPIAR-10315 |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 11667.305 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 #2: Protein | Mass: 502246.719 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: thigh #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-CA / Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: 3D ARRAY / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Ryanodine receptor 1 bound to FKBP1B / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES |
---|---|
Molecular weight | Value: 2.3 MDa / Experimental value: NO |
Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid type: UltrAuFoil |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Specimen holder | Cryogen: NITROGEN Specimen holder model: GATAN ULTST ULTRA LOW TEMPERATURE SINGLE TILT HELIUM COOLING HOLDER |
Image recording | Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||
3D reconstruction | Resolution: 4.5 Å / Resolution method: OTHER / Num. of particles: 791956 Details: RESMAP and visual inspection. FSC not possible as no half-sets are available with the manifold embedding method Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL Details: fitted to a model domain by domain with the rigid-body fit function in COOT 71, using multiple starting models to avoid model bias (PDB ID: 5TB4, 5T9R, 5TAP, 5T9V, 5TAL, 5TAQ) 22. The models ...Details: fitted to a model domain by domain with the rigid-body fit function in COOT 71, using multiple starting models to avoid model bias (PDB ID: 5TB4, 5T9R, 5TAP, 5T9V, 5TAL, 5TAQ) 22. The models were then refined in real-space using phenix.real_space_refine | ||||||||||||
Atomic model building | PDB-ID: 5TB4 Accession code: 5TB4 / Source name: PDB / Type: experimental model |