+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6106 | |||||||||
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Title | Cryo-EM structure of calstabin-bound RYR1-EGTA (class 2) | |||||||||
Map data | Reconstruction with C4 symmetry imposed of class 2 of the RYR1-EGTA dataset filtered at 4.8A and sharpened with a B factor of -214 | |||||||||
Sample |
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Keywords | calcium release / excitation-contraction coupling in muscle / closed-state / alpha solenoid scaffold / six-transmembrane ion channel / EF-hands / calstabin / FKBP12 / SPRY | |||||||||
Function / homology | Function and homology information protein binding / ATP-gated ion channel activity / terminal cisterna / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / skin development / organelle membrane / cellular response to caffeine ...protein binding / ATP-gated ion channel activity / terminal cisterna / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / skin development / organelle membrane / cellular response to caffeine / outflow tract morphogenesis / intracellularly gated calcium channel activity / toxic substance binding / smooth endoplasmic reticulum / voltage-gated calcium channel activity / skeletal muscle fiber development / monoatomic ion transport / striated muscle contraction / muscle contraction / release of sequestered calcium ion into cytosol / sarcoplasmic reticulum membrane / cellular response to calcium ion / sarcoplasmic reticulum / calcium ion transmembrane transport / calcium channel activity / sarcolemma / transmembrane transport / Z disc / intracellular calcium ion homeostasis / disordered domain specific binding / monoatomic ion channel activity / protein homotetramerization / transmembrane transporter binding / membrane => GO:0016020 / calmodulin binding / calcium ion binding / ATP binding / identical protein binding / membrane Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.8 Å | |||||||||
Authors | Zalk R / Clarke OB / des Georges A / Grassucci RA / Reiken S / Mancia F / Hendrickson WA / Frank J / Marks AR | |||||||||
Citation | Journal: Nature / Year: 2015 Title: Structure of a mammalian ryanodine receptor. Authors: Ran Zalk / Oliver B Clarke / Amédée des Georges / Robert A Grassucci / Steven Reiken / Filippo Mancia / Wayne A Hendrickson / Joachim Frank / Andrew R Marks / Abstract: Ryanodine receptors (RyRs) mediate the rapid release of calcium (Ca(2+)) from intracellular stores into the cytosol, which is essential for numerous cellular functions including excitation- ...Ryanodine receptors (RyRs) mediate the rapid release of calcium (Ca(2+)) from intracellular stores into the cytosol, which is essential for numerous cellular functions including excitation-contraction coupling in muscle. Lack of sufficient structural detail has impeded understanding of RyR gating and regulation. Here we report the closed-state structure of the 2.3-megadalton complex of the rabbit skeletal muscle type 1 RyR (RyR1), solved by single-particle electron cryomicroscopy at an overall resolution of 4.8 Å. We fitted a polyalanine-level model to all 3,757 ordered residues in each protomer, defining the transmembrane pore in unprecedented detail and placing all cytosolic domains as tertiary folds. The cytosolic assembly is built on an extended α-solenoid scaffold connecting key regulatory domains to the pore. The RyR1 pore architecture places it in the six-transmembrane ion channel superfamily. A unique domain inserted between the second and third transmembrane helices interacts intimately with paired EF-hands originating from the α-solenoid scaffold, suggesting a mechanism for channel gating by Ca(2+). | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6106.map.gz | 112.5 MB | EMDB map data format | |
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Header (meta data) | emd-6106-v30.xml emd-6106.xml | 12.4 KB 12.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_6106_fsc.xml emd_6106_fsc_1.xml | 10.9 KB 11.6 KB | Display Display | FSC data file |
Images | 400_6106.gif 80_6106.gif | 64.4 KB 3.8 KB | ||
Others | emd_6106_additional_1.map.gz | 111.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6106 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6106 | HTTPS FTP |
-Validation report
Summary document | emd_6106_validation.pdf.gz | 79.1 KB | Display | EMDB validaton report |
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Full document | emd_6106_full_validation.pdf.gz | 78.2 KB | Display | |
Data in XML | emd_6106_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6106 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6106 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_6106.map.gz / Format: CCP4 / Size: 117.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction with C4 symmetry imposed of class 2 of the RYR1-EGTA dataset filtered at 4.8A and sharpened with a B factor of -214 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.66 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Supplemental map: emd 6106 additional 1.map
File | emd_6106_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : rabbit skeletal muscle type 1 RyR (RyR1), EGTA-treated, bound to ...
Entire | Name: rabbit skeletal muscle type 1 RyR (RyR1), EGTA-treated, bound to calstabin2 (FKBP12.6) |
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Components |
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-Supramolecule #1000: rabbit skeletal muscle type 1 RyR (RyR1), EGTA-treated, bound to ...
Supramolecule | Name: rabbit skeletal muscle type 1 RyR (RyR1), EGTA-treated, bound to calstabin2 (FKBP12.6) type: sample / ID: 1000 / Oligomeric state: heterooctamer / Number unique components: 2 |
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Molecular weight | Theoretical: 3 MDa / Method: sequence |
-Macromolecule #1: Ryanodine Receptor 1
Macromolecule | Name: Ryanodine Receptor 1 / type: protein_or_peptide / ID: 1 / Name.synonym: RYR1 / Details: Closed state, EGTA treated / Number of copies: 4 / Oligomeric state: Tetramer / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) / synonym: rabbit / Tissue: skeletal muscle |
Molecular weight | Experimental: 2.2 MDa / Theoretical: 2.2 MDa |
Sequence | UniProtKB: Ryanodine receptor 1 GO: intracellular calcium ion homeostasis, ryanodine-sensitive calcium-release channel activity, membrane => GO:0016020, monoatomic ion transport, transmembrane transport, calcium ion transmembrane ...GO: intracellular calcium ion homeostasis, ryanodine-sensitive calcium-release channel activity, membrane => GO:0016020, monoatomic ion transport, transmembrane transport, calcium ion transmembrane transport, monoatomic ion channel activity, calcium channel activity, calcium ion binding, protein binding InterPro: Ryanodine receptor, SPRY domain, B30.2/SPRY domain, EF-hand domain pair, Ion transport domain |
-Macromolecule #2: Peptidyl-prolyl cis-trans isomerase FKBP1B
Macromolecule | Name: Peptidyl-prolyl cis-trans isomerase FKBP1B / type: protein_or_peptide / ID: 2 / Name.synonym: Calstabin-2, FKBP-12.6 / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: human |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 8 mg/mL |
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Buffer | pH: 7.5 Details: 10 mM HEPES, pH 7.5, 1% w/v CHAPS, 1 M NaCl, 2 mM TCEP, 5 mM EGTA, 0.25% w/v CHAPS, 0.001% w/v DOPC (Avanti) |
Grid | Details: C-flat CF-1.2/1.3-2C-T, Protochips Inc, NC |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 95 K / Instrument: FEI VITROBOT MARK IV / Method: Wait 30 seconds, blot 1.5 seconds, then plunge. |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 180,000 times magnification. |
Details | 8 second exposure, 23 frames |
Date | Jul 1, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 3423 / Average electron dose: 25 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 31558 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: -4.0 µm / Nominal defocus min: -1.0 µm / Nominal magnification: 23000 |
Sample stage | Specimen holder model: GATAN HELIUM |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |