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- 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
TitleStructure of the ryanodine receptor at resolution of 6.1 A in closed state
ComponentsRYANODINE RECEPTOR 1
KeywordsSIGNALING 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 / cellular response to caffeine / intracellularly gated calcium channel activity / 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 / cellular response to caffeine / intracellularly gated calcium channel activity / outflow tract morphogenesis / organelle membrane / toxic substance binding / voltage-gated calcium channel activity / skeletal muscle fiber development / release of sequestered calcium ion into cytosol / sarcoplasmic reticulum membrane / cellular response to calcium ion / muscle contraction / sarcoplasmic reticulum / calcium ion transmembrane transport / calcium channel activity / intracellular calcium ion homeostasis / disordered domain specific binding / protein homotetramerization / transmembrane transporter binding / calmodulin binding / calcium ion binding / ATP binding / membrane / identical protein binding
Similarity search - Function
: / Ryanodine receptor junctional solenoid repeat / Ryanodine receptor, SPRY domain 2 / Ryanodine Receptor TM 4-6 / Ryanodine receptor / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor, SPRY domain 3 / Ryanodine Receptor TM 4-6 / Ryanodine receptor Ryr / RyR domain ...: / Ryanodine receptor junctional solenoid repeat / Ryanodine receptor, SPRY domain 2 / Ryanodine Receptor TM 4-6 / Ryanodine receptor / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor, SPRY domain 3 / Ryanodine Receptor TM 4-6 / Ryanodine receptor Ryr / RyR domain / RyR/IP3 receptor binding core, RIH domain superfamily / : / RyR/IP3R Homology associated domain / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / RyR and IP3R Homology associated / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / MIR motif / MIR domain / MIR domain profile. / Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases / Mir domain superfamily / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Ryanodine receptor 1
Similarity search - Component
Biological speciesORYCTOLAGUS CUNICULUS (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.1 Å
AuthorsEfremov, R.G. / Leitner, A. / Aebersold, R. / Raunser, S.
CitationJournal: 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
DepositionAug 11, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Jan 21, 2015Group: Database references
Revision 1.3Aug 2, 2017Group: Data collection / Category: em_imaging / em_software
Item: _em_imaging.nominal_defocus_max / _em_imaging.nominal_defocus_min ..._em_imaging.nominal_defocus_max / _em_imaging.nominal_defocus_min / _em_software.fitting_id / _em_software.image_processing_id / _em_software.name
Revision 1.4Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
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.

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Structure visualization

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Assembly

Deposited unit
A: RYANODINE RECEPTOR 1
B: RYANODINE RECEPTOR 1
C: RYANODINE RECEPTOR 1
D: RYANODINE RECEPTOR 1


Theoretical massNumber of molelcules
Total (without water)1,894,5164
Polymers1,894,5164
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Protein
RYANODINE RECEPTOR 1 / / RYR-1 / RYR1 / SKELETAL MUSCLE CALCIUM RELEASE CHANNEL / SKELETAL MUSCLE RYANODINE RECEPTOR / ...RYR-1 / RYR1 / SKELETAL MUSCLE CALCIUM RELEASE CHANNEL / SKELETAL MUSCLE RYANODINE RECEPTOR / SKELETAL MUSCLE-TYPE RYANODINE RECEPTOR / TYPE 1 RYANODINE RECEPTOR


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: MUSCLESkeletal muscle / References: UniProt: P11716

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: RYANODINE RECEPTOR 1 / Type: COMPLEX
Buffer solutionName: 10 MM MOPS, 200MM NACL, 2MM DTT, 1MM EGTA / pH: 7.4 / Details: 10 MM MOPS, 200MM NACL, 2MM DTT, 1MM EGTA
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Feb 3, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 47000 X / Calibrated magnification: 47992 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 0 mm
Specimen holderTemperature: 80 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansNum. digital images: 2000

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Processing

EM software
IDNameCategory
1UCSF Chimeramodel fitting
2RELION3D reconstruction
3SPARX3D reconstruction
CTF correctionDetails: FULL CORRECTION
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionMethod: 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 buildingProtocol: OTHER / Space: REAL / Details: METHOD--LOCAL REFINEMENT
RefinementHighest resolution: 6.1 Å
Refinement stepCycle: LAST / Highest resolution: 6.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms81640 0 0 0 81640

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