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- EMDB-10642: Structure of rabbit ryanodine receptor 1 in apo state in native m... -

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Basic information

Entry
Database: EMDB / ID: EMD-10642
TitleStructure of rabbit ryanodine receptor 1 in apo state in native membrane (class 1)
Map dataStructure of rabbit ryanodine receptor 1 in apo state in native membrane (class 1)
Sample
  • Complex: Rabbit ryanodine receptor 1 in apo state in native membrane
Biological speciesOryctolagus cuniculus (rabbit)
Methodsubtomogram averaging / cryo EM / Resolution: 15.4 Å
AuthorsChen W / Kudryashev M
Funding support Germany, 1 items
OrganizationGrant numberCountry
Alexander von Humboldt FoundationSofja Kovalevskaja Award to Misha Kudryashev Germany
CitationJournal: EMBO Rep / Year: 2020
Title: Structure of RyR1 in native membranes.
Authors: Wenbo Chen / Mikhail Kudryashev /
Abstract: Ryanodine receptor 1 (RyR1) mediates excitation-contraction coupling by releasing Ca from sarcoplasmic reticulum (SR) to the cytoplasm of skeletal muscle cells. RyR1 activation is regulated by ...Ryanodine receptor 1 (RyR1) mediates excitation-contraction coupling by releasing Ca from sarcoplasmic reticulum (SR) to the cytoplasm of skeletal muscle cells. RyR1 activation is regulated by several proteins from both the cytoplasm and lumen of the SR. Here, we report the structure of RyR1 from native SR membranes in closed and open states. Compared to the previously reported structures of purified RyR1, our structure reveals helix-like densities traversing the bilayer approximately 5 nm from the RyR1 transmembrane domain and sarcoplasmic extensions linking RyR1 to a putative calsequestrin network. We document the primary conformation of RyR1 in situ and its structural variations. The activation of RyR1 is associated with changes in membrane curvature and movement in the sarcoplasmic extensions. Our results provide structural insight into the mechanism of RyR1 in its native environment.
History
DepositionJan 24, 2020-
Header (metadata) releaseMar 18, 2020-
Map releaseMar 18, 2020-
UpdateMay 13, 2020-
Current statusMay 13, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.273
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.273
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10642.png

Downloads & links

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Map

FileDownload / File: emd_10642.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of rabbit ryanodine receptor 1 in apo state in native membrane (class 1)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.7 Å/pix.
x 200 pix.
= 540. Å		2.7 Å/pix.
x 200 pix.
= 540. Å		2.7 Å/pix.
x 200 pix.
= 540. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.273 / Movie #1: 0.273
Minimum - Maximum-1.4138962 - 1.5417366
Average (Standard dev.)0.009953464 (±0.14334062)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 540.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.72.72.7
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z540.000540.000540.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-1.3601.6290.005

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Supplemental data

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Half map: Structure of rabbit ryanodine receptor 1 in apo...

Fileemd_10642_half_map_1.map
AnnotationStructure of rabbit ryanodine receptor 1 in apo state in native membrane (class 1, half map2)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Structure of rabbit ryanodine receptor 1 in apo...

Fileemd_10642_half_map_2.map
AnnotationStructure of rabbit ryanodine receptor 1 in apo state in native membrane (class 1, half map1)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Rabbit ryanodine receptor 1 in apo state in native membrane

EntireName: Rabbit ryanodine receptor 1 in apo state in native membrane
Components
  • Complex: Rabbit ryanodine receptor 1 in apo state in native membrane

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Supramolecule #1: Rabbit ryanodine receptor 1 in apo state in native membrane

SupramoleculeName: Rabbit ryanodine receptor 1 in apo state in native membrane
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / Tissue: skeletal muscle / Organelle: sarcoplasmic reticulum

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statetissue

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Sample preparation

BufferpH: 7.1
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 15.4 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Dynamo / Number subtomograms used: 1138
ExtractionNumber tomograms: 82 / Number images used: 1138 / Software: (Name: IMOD, Dynamo)
CTF correctionSoftware - Name: Gctf
Final 3D classificationSoftware - Name: Dynamo
Final angle assignmentType: OTHER / Software - Name: Dynamo / Details: subtomogram alignment using Dynamo

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