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- PDB-4uwe: Structure of the ryanodine receptor at resolution of 8.5 A in par... -

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Basic information

Entry
Database: PDB / ID: 4uwe
TitleStructure of the ryanodine receptor at resolution of 8.5 A in partially open state
ComponentsRYANODINE RECEPTOR 1
KeywordsSIGNALING PROTEIN / CALCIUM BINDING / ION CHANNEL / MUSCULAR CONTRACTION / CONFORMATIONAL CHANGES.
Function / homology
Function and homology information


ATP-gated ion channel activity / terminal cisterna / ryanodine-sensitive calcium-release channel activity / ryanodine receptor complex / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / cellular response to caffeine / skin development / organelle membrane / smooth endoplasmic reticulum ...ATP-gated ion channel activity / terminal cisterna / ryanodine-sensitive calcium-release channel activity / ryanodine receptor complex / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / cellular response to caffeine / skin development / organelle membrane / smooth endoplasmic reticulum / intracellularly gated calcium channel activity / outflow tract morphogenesis / toxic substance binding / striated muscle contraction / 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 / sarcolemma / calcium ion transmembrane transport / calcium channel activity / 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
Ryanodine receptor, SPRY domain 2 / : / Ryanodine receptor junctional solenoid repeat / 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, SPRY domain 2 / : / Ryanodine receptor junctional solenoid repeat / 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. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / 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: 8.5 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 30, 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
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _struct_sheet.number_strands
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
Water00
1


  • Idetical with deposited unit
  • defined by author&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: 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, 200 MM NACL, 2 MM DTT AND 10 MM CACL2, 0.2% FLUORINATED OCTYL- MALTOSIDE
pH: 7.4
Details: 10 MM MOPS, 200 MM NACL, 2 MM DTT AND 10 MM CACL2, 0.2% FLUORINATED OCTYL- MALTOSIDE
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL 3200FSC / Date: Mar 12, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 X / Calibrated magnification: 58610 X / Nominal defocus max: 3900 nm / Nominal defocus min: 900 nm / Cs: 4.1 mm
Specimen holderTemperature: 80 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k)
Image scansNum. digital images: 1041

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Processing

EM software
IDNameCategory
1UCSF Chimeramodel fitting
2SPARX3D reconstruction
CTF correctionDetails: FULL CORRECTION
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionMethod: BACKPROJECTION / Resolution: 8.5 Å / Num. of particles: 94354 / Nominal pixel size: 2.53 Å / Actual pixel size: 2.59 Å
Magnification calibration: CROSS CORRELATION WITH A MAP CALCULATED FROM CRYSTAL STRUCTURE OF ABC DOMAIN
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2752. (DEPOSITION ID: 12779).
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--EM
Atomic model buildingPDB-ID: 2UWA

2uwa


Accession code: 2UWA / Source name: PDB / Type: experimental model
RefinementHighest resolution: 8.5 Å
Refinement stepCycle: LAST / Highest resolution: 8.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms81600 0 0 0 81600

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