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Yorodumi- PDB-4uwa: Structure of the ryanodine receptor at resolution of 6.1 A in clo... -
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-Basic information
Entry | Database: PDB / ID: 4uwa | ||||||
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Title | Structure of the ryanodine receptor at resolution of 6.1 A in closed state | ||||||
Components | RYANODINE RECEPTOR 1 | ||||||
Keywords | SIGNALING PROTEIN / SIGANLING PRTEIN / CALCIUM BINDING / ION CHANNEL / MUSCULAR CONTRACTION / CONFORMATIONAL CHANGES. | ||||||
Function / homology | Function and homology information 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 ...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 / 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 / Z disc / intracellular calcium ion homeostasis / disordered domain specific binding / protein homotetramerization / transmembrane transporter binding / calmodulin binding / calcium ion binding / ATP binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | ORYCTOLAGUS CUNICULUS (rabbit) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.1 Å | ||||||
Authors | Efremov, R.G. / Leitner, A. / Aebersold, R. / Raunser, S. | ||||||
Citation | Journal: Nature / Year: 2015 Title: Architecture and conformational switch mechanism of the ryanodine receptor. Authors: Rouslan G Efremov / Alexander Leitner / Ruedi Aebersold / Stefan Raunser / Abstract: Muscle contraction is initiated by the release of calcium (Ca(2+)) from the sarcoplasmic reticulum into the cytoplasm of myocytes through ryanodine receptors (RyRs). RyRs are homotetrameric channels ...Muscle contraction is initiated by the release of calcium (Ca(2+)) from the sarcoplasmic reticulum into the cytoplasm of myocytes through ryanodine receptors (RyRs). RyRs are homotetrameric channels with a molecular mass of more than 2.2 megadaltons that are regulated by several factors, including ions, small molecules and proteins. Numerous mutations in RyRs have been associated with human diseases. The molecular mechanism underlying the complex regulation of RyRs is poorly understood. Using electron cryomicroscopy, here we determine the architecture of rabbit RyR1 at a resolution of 6.1 Å. We show that the cytoplasmic moiety of RyR1 contains two large α-solenoid domains and several smaller domains, with folds suggestive of participation in protein-protein interactions. The transmembrane domain represents a chimaera of voltage-gated sodium and pH-activated ion channels. We identify the calcium-binding EF-hand domain and show that it functions as a conformational switch allosterically gating the channel. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 4uwa.cif.gz | 1.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4uwa.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 4uwa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uwa_validation.pdf.gz | 919.1 KB | Display | wwPDB validaton report |
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Full document | 4uwa_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 4uwa_validation.xml.gz | 277.7 KB | Display | |
Data in CIF | 4uwa_validation.cif.gz | 455.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/4uwa ftp://data.pdbj.org/pub/pdb/validation_reports/uw/4uwa | HTTPS FTP |
-Related structure data
Related structure data | 2751MC 2752C 4uweC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 473628.906 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Cell: MYOCYTE / Organ: SARCOPLASMIC RETICULUM / Tissue: MUSCLE / References: UniProt: P11716 |
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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: RYANODINE RECEPTOR 1 / Type: COMPLEX |
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Buffer solution | Name: 10 MM MOPS, 200MM NACL, 2MM DTT, 1MM EGTA / pH: 7.4 / Details: 10 MM MOPS, 200MM NACL, 2MM DTT, 1MM EGTA |
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: LIQUID ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Feb 3, 2014 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 47000 X / Calibrated magnification: 47992 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 0 mm |
Specimen holder | Temperature: 80 K |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
Image scans | Num. digital images: 2000 |
-Processing
EM software |
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CTF correction | Details: FULL CORRECTION | ||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||
3D reconstruction | Method: BACKPROJECTION / Resolution: 6.1 Å / Num. of particles: 25000 / Nominal pixel size: 1.45 Å / Actual pixel size: 1.42 Å Magnification calibration: CROSS CORRELATION WITH A MAP CALCULATED FROM CRYSTAL STRUCTURE OF ABC DOMAIN Details: THE MODEL WAS BUILD BY RIGID BODY DOCKING OF CRYSTAL STRUCTURES OF ABC DOMAIN PDB CODE 2 AOX, RESIDUES 1-394, REPEAT 3-4 DOMAIN(PHOSPHORYLATION DOMAIN), RESIDUES 2,734- 2,939, PDB CODE 4ERT, ...Details: THE MODEL WAS BUILD BY RIGID BODY DOCKING OF CRYSTAL STRUCTURES OF ABC DOMAIN PDB CODE 2 AOX, RESIDUES 1-394, REPEAT 3-4 DOMAIN(PHOSPHORYLATION DOMAIN), RESIDUES 2,734- 2,939, PDB CODE 4ERT, REPEAT 1-2 DOMAIN, RESIDUES 851-1, 053, HOMOLOGY MODELLED BASED ON CRYSTAL STRUCTURE OF REPEAT3-4 DOMAIN, EF-HAND DOMAIN,RESIDUES 4,084-4,135, HOMOLOGY MODELLED IN PHYRE2, SPRY1 DOMAIN , RESIDUES 646- 842, SPRY2 DOMAIN , RESIDUES 1,070-1,310, AND SPRY 3 DOMAIN, RESIDUES 1,420-1,571,WERE MODELLED IN ROBETTA. THE REST OF THE MODEL WAS BUILT AS POLY ALANINE CHAIN FOR WHICH APPOXIMATE RESIDUE NUMBERS ARE GIVEN. IN ADDITION FOR THE ALPHA-SOLENOID 2 DOMAIN, RESIDUES CA.1,920-2,730 AND CA. 2,940-3,500, THE DIRECTIONALITY OF THE CHAIN IS NOT KNOWN. SEQUENCE OF CHAINS A,B,C,D MGDGGEGEDEVQFLRTDDEVVLQCSATVLKEQLKLCLAAEGFGNRLCFLEPTSNAQNVPPDLAICCFT SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2751. (DEPOSITION ID: 12695). Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL / Details: METHOD--LOCAL REFINEMENT | ||||||||||||
Refinement | Highest resolution: 6.1 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 6.1 Å
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