[English] 日本語
Yorodumi- PDB-8vk4: Structure of mouse RyR1 in complex with S100A1 (high-Ca2+/CFF/ATP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vk4 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of mouse RyR1 in complex with S100A1 (high-Ca2+/CFF/ATP dataset) | ||||||
Components |
| ||||||
Keywords | MEMBRANE PROTEIN / Calcium / Ion Channel | ||||||
Function / homology | Function and homology information junctional membrane complex / TGF-beta receptor signaling activates SMADs / Calcineurin activates NFAT / mTORC1-mediated signalling / activin receptor binding / cytoplasmic side of membrane / regulation of muscle contraction / calcium-induced calcium release activity / sarcoplasmic reticulum calcium ion transport / regulation of response to osmotic stress ...junctional membrane complex / TGF-beta receptor signaling activates SMADs / Calcineurin activates NFAT / mTORC1-mediated signalling / activin receptor binding / cytoplasmic side of membrane / regulation of muscle contraction / calcium-induced calcium release activity / sarcoplasmic reticulum calcium ion transport / regulation of response to osmotic stress / transforming growth factor beta receptor binding / signaling receptor inhibitor activity / Stimuli-sensing channels / type I transforming growth factor beta receptor binding / Ion homeostasis / heart trabecula formation / terminal cisterna / ryanodine receptor complex / I-SMAD binding / ryanodine-sensitive calcium-release channel activity / I band / S100 protein binding / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / response to caffeine / regulation of heart contraction / skin development / cellular response to ATP / ventricular cardiac muscle tissue morphogenesis / FK506 binding / positive regulation of sprouting angiogenesis / cellular response to caffeine / outflow tract morphogenesis / smooth endoplasmic reticulum / organelle membrane / striated muscle contraction / voltage-gated calcium channel activity / T cell proliferation / skeletal muscle fiber development / axon terminus / heart morphogenesis / release of sequestered calcium ion into cytosol / regulation of ryanodine-sensitive calcium-release channel activity / Hsp70 protein binding / sarcoplasmic reticulum membrane / T-tubule / calcium channel complex / regulation of cytosolic calcium ion concentration / cellular response to calcium ion / extrinsic component of cytoplasmic side of plasma membrane / sarcomere / sarcoplasmic reticulum / muscle contraction / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / negative regulation of transforming growth factor beta receptor signaling pathway / sarcolemma / calcium channel activity / cytoplasmic side of plasma membrane / Z disc / cytokine-mediated signaling pathway / calcium ion transport / cell cortex / ATPase binding / protein homotetramerization / protease binding / vesicle / transmembrane transporter binding / response to hypoxia / calmodulin binding / synapse / calcium ion binding / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / protein homodimerization activity / protein-containing complex / mitochondrion / nucleoplasm / ATP binding / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.56 Å | ||||||
Authors | Weninger, G. / Marks, A.R. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: To Be Published Title: Structural insights into the regulation of RyR1 by S100A1. Authors: Weninger, G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8vk4.cif.gz | 3.1 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8vk4.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8vk4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vk/8vk4 ftp://data.pdbj.org/pub/pdb/validation_reports/vk/8vk4 | HTTPS FTP |
---|
-Related structure data
Related structure data | 43304MC 8vjjC 8vjkC C: citing same article (ref.) M: map data used to model this data |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Protein , 3 types, 16 molecules EFGHIJKLNMOPDABC
#1: Protein | Mass: 11939.629 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P26883, peptidylprolyl isomerase #2: Protein | Mass: 10516.784 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: S100a1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q91V77 #3: Protein | Mass: 565692.562 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: E9PZQ0 |
---|
-Non-polymers , 5 types, 44 molecules
#4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-ZN / #6: Chemical | ChemComp-CFF / #7: Chemical | ChemComp-ATP / #8: Chemical | ChemComp-PCW / |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Complex of RyR1 with Calstabin-1 and S100A1 (high-Ca2+/CFF/ATP condition) Type: COMPLEX / Details: 0.25 mM free Ca2+; 5 mM Caffeine; 10 mM ATP / Entity ID: #1-#3 / Source: NATURAL | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Source (natural) | Organism: Mus musculus (house mouse) | |||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.4 | |||||||||||||||||||||||||||||||||||
Buffer component |
| |||||||||||||||||||||||||||||||||||
Specimen | Conc.: 8.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 0.15 mmol/L S100A1-dimer | |||||||||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1 | |||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1200 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 58 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 12555 |
-Processing
EM software |
| |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31572 / Symmetry type: POINT |