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- EMDB-37089: The in-situ map of RyR1 in skeletal muscle of mouse -

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Basic information

Entry
Database: EMDB / ID: EMD-37089
TitleThe in-situ map of RyR1 in skeletal muscle of mouse
Map dataThe in-situ map of RyR1 in skeletal muscle of mouse
Sample
  • Tissue: Tissue of the mouse skeletal muscle
KeywordsCalcium Channel / Triad junctions / Excitation-contraction coupling / In-situ / MEMBRANE PROTEIN
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 16.7 Å
AuthorsSun F / Zhu Y / Xu J
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Adv / Year: 2024
Title: In situ structural insights into the excitation-contraction coupling mechanism of skeletal muscle.
Authors: Jiashu Xu / Chenyi Liao / Chang-Cheng Yin / Guohui Li / Yun Zhu / Fei Sun /
Abstract: Excitation-contraction coupling (ECC) is a fundamental mechanism in control of skeletal muscle contraction and occurs at triad junctions, where dihydropyridine receptors (DHPRs) on transverse tubules ...Excitation-contraction coupling (ECC) is a fundamental mechanism in control of skeletal muscle contraction and occurs at triad junctions, where dihydropyridine receptors (DHPRs) on transverse tubules sense excitation signals and then cause calcium release from the sarcoplasmic reticulum via coupling to type 1 ryanodine receptors (RyR1s), inducing the subsequent contraction of muscle filaments. However, the molecular mechanism remains unclear due to the lack of structural details. Here, we explored the architecture of triad junction by cryo-electron tomography, solved the in situ structure of RyR1 in complex with FKBP12 and calmodulin with the resolution of 16.7 Angstrom, and found the intact RyR1-DHPR supercomplex. RyR1s arrange into two rows on the terminal cisternae membrane by forming right-hand corner-to-corner contacts, and tetrads of DHPRs bind to RyR1s in an alternating manner, forming another two rows on the transverse tubule membrane. This unique arrangement is important for synergistic calcium release and provides direct evidence of physical coupling in ECC.
History
DepositionAug 5, 2023-
Header (metadata) releaseApr 3, 2024-
Map releaseApr 3, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_37089.png

Downloads & links

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Map

FileDownload / File: emd_37089.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe in-situ map of RyR1 in skeletal muscle of mouse
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.44 Å/pix.
x 128 pix.
= 568.32 Å		4.44 Å/pix.
x 128 pix.
= 568.32 Å		4.44 Å/pix.
x 128 pix.
= 568.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.44 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-0.7445377 - 0.9736302
Average (Standard dev.)0.015406493 (±0.16667913)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 568.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: The half map of the in-situ RyR1 in skeletal muscle of mouse

Fileemd_37089_half_map_1.map
AnnotationThe half map of the in-situ RyR1 in skeletal muscle of mouse
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The half map of the in-situ RyR1 in skeletal muscle of mouse

Fileemd_37089_half_map_2.map
AnnotationThe half map of the in-situ RyR1 in skeletal muscle of mouse
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tissue of the mouse skeletal muscle

EntireName: Tissue of the mouse skeletal muscle
Components
  • Tissue: Tissue of the mouse skeletal muscle

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Supramolecule #1: Tissue of the mouse skeletal muscle

SupramoleculeName: Tissue of the mouse skeletal muscle / type: tissue / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse) / Strain: Kunming mouse

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 70 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 90 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 4.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 4.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 16.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 1365
ExtractionNumber tomograms: 230 / Number images used: 4080
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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