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- EMDB-2752: Structure of the ryanodine receptor at resolution of 8.5 A in par... -

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Basic information

Entry
Database: EMDB / ID: EMD-2752
TitleStructure of the ryanodine receptor at resolution of 8.5 A in partially open state
Map datareconstruction of ryanodine receptor 1 in partially open state
Sample
  • Sample: Ryanodine receptor 1 (calcium release channel) from rabbit
  • Protein or peptide: Ryanodine receptor 1
Keywordscalcium 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 / voltage-gated calcium channel activity / smooth endoplasmic reticulum / skeletal muscle fiber development / striated muscle contraction / release of sequestered calcium ion into cytosol / muscle contraction / 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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.5 Å
AuthorsEfremov RG / 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, 2014-
Header (metadata) releaseSep 10, 2014-
Map releaseDec 10, 2014-
UpdateJan 14, 2015-
Current statusJan 14, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-4uwe
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2752.jpg

Downloads & links

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Map

FileDownload / File: emd_2752.map.gz / Format: CCP4 / Size: 41.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationreconstruction of ryanodine receptor 1 in partially open state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.59 Å/pix.
x 224 pix.
= 580.16 Å		2.59 Å/pix.
x 224 pix.
= 580.16 Å		2.59 Å/pix.
x 224 pix.
= 580.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.59 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 1.31 / Movie #1: 1.5
Minimum - Maximum-8.40281105 - 9.765976909999999
Average (Standard dev.)0.02009332 (±0.32368639)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-112-112-112
Dimensions224224224
Spacing224224224
CellA=B=C: 580.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.592.592.59
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z580.160580.160580.160
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ442626
MAP C/R/S123
start NC/NR/NS-112-112-112
NC/NR/NS224224224
D min/max/mean-8.4039.7660.020

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Supplemental data

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Segmentation: mask used for calculating FSC curve

Annotationmask used for calculating FSC curve
Fileemd_2752_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ryanodine receptor 1 (calcium release channel) from rabbit

EntireName: Ryanodine receptor 1 (calcium release channel) from rabbit
Components
  • Sample: Ryanodine receptor 1 (calcium release channel) from rabbit
  • Protein or peptide: Ryanodine receptor 1

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Supramolecule #1000: Ryanodine receptor 1 (calcium release channel) from rabbit

SupramoleculeName: Ryanodine receptor 1 (calcium release channel) from rabbit
type: sample / ID: 1000 / Details: protein was reconstituted in lipid nanodiscs / Oligomeric state: tetramer / Number unique components: 1
Molecular weightTheoretical: 2.26 MDa

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Macromolecule #1: Ryanodine receptor 1

MacromoleculeName: Ryanodine receptor 1 / type: protein_or_peptide / ID: 1 / Name.synonym: Skeletal muscle calcium release channel / Number of copies: 4 / Oligomeric state: tetramer / Recombinant expression: No
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: muscle / Organelle: Sarcoplasmic reticulum / Location in cell: Sarcoplasmic reticulum membrane
Molecular weightTheoretical: 2.26 MDa
SequenceUniProtKB: Ryanodine receptor 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 7.4
Details: 10 mM MOPS, 200 mM NaCl, 10mM CaCl2, 2mM DTT, 0.2% fluorinated octyl-maltoside
GridDetails: C-Flat CF-1.2/1.3-4C holey carbon grid
VitrificationCryogen name: ETHANE / Instrument: GATAN CRYOPLUNGE 3
Method: protein solution was applied on glow discharged grid and blotted for 1.5 seconds before plunging

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Electron microscopy

MicroscopeJEOL 3200FSC
TemperatureMin: 80 K
Specialist opticsEnergy filter - Name: in-column omega energy filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 15.0 eV
DateMar 12, 2012
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k) / Number real images: 1041 / Average electron dose: 20 e/Å2
Details: Images were collected automatically with EM-TOOLS software
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal defocus max: 0.0039 µm / Nominal defocus min: 0.0009 µm / Nominal magnification: 60000
Sample stageSpecimen holder: liquid nitorgen cooled / Specimen holder model: JEOL 3200FSC CRYOHOLDER

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Image processing

DetailsDefocus of the micrographs was determined in CTFFIND, particles were picked in SIGNATURE, 3D reconstruction was calculated in SPARX
CTF correctionDetails: full correction
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.5 Å / Resolution method: OTHER / Software - Name: SPARX / Number images used: 94354
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

2uwa

SoftwareName: Chimera
Detailsmodel obtained by rigid body fitting of domains of the structure 2uwa
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-4uwe:
Structure of the ryanodine receptor at resolution of 8.5 A in partially open state

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