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- EMDB-43297: Constituent EM map: Focused refinement BSol+S100A1 of mouse RyR1 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-43297
TitleConstituent EM map: Focused refinement BSol+S100A1 of mouse RyR1 in complex with S100A1 (EGTA-only dataset)
Map dataConstituent EM map: Focused refinement BSol/S100A1 of mouse RyR1 in complex with S100A1 (EGTA-only dataset)
Sample
  • Complex: Complex of RyR1 with Calstabin-1 and S100A1 (EGTA condition)
KeywordsCalcium / Ion Channel / Complex / MEMBRANE PROTEIN
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsWeninger G / Marks AR
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL145473 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Structural insights into the regulation of RyR1 by S100A1.
Authors: Gunnar Weninger / Marco C Miotto / Carl Tchagou / Steven Reiken / Haikel Dridi / Sören Brandenburg / Gabriel C Riedemann / Qi Yuan / Yang Liu / Alexander Chang / Anetta Wronska / Stephan E ...Authors: Gunnar Weninger / Marco C Miotto / Carl Tchagou / Steven Reiken / Haikel Dridi / Sören Brandenburg / Gabriel C Riedemann / Qi Yuan / Yang Liu / Alexander Chang / Anetta Wronska / Stephan E Lehnart / Andrew R Marks /
Abstract: S100A1, a small homodimeric EF-hand Ca-binding protein (~21 kDa), plays an important regulatory role in Ca signaling pathways involved in various biological functions including Ca cycling and ...S100A1, a small homodimeric EF-hand Ca-binding protein (~21 kDa), plays an important regulatory role in Ca signaling pathways involved in various biological functions including Ca cycling and contractile performance in skeletal and cardiac myocytes. One key target of the S100A1 interactome is the ryanodine receptor (RyR), a huge homotetrameric Ca release channel (~2.3 MDa) of the sarcoplasmic reticulum. Here, we report cryoelectron microscopy structures of S100A1 bound to RyR1, the skeletal muscle isoform, in absence and presence of Ca. Ca-free apo-S100A1 binds beneath the bridging solenoid (BSol) and forms contacts with the junctional solenoid and the shell-core linker of RyR1. Upon Ca-binding, S100A1 undergoes a conformational change resulting in the exposure of the hydrophobic pocket known to serve as a major interaction site of S100A1. Through interactions of the hydrophobic pocket with RyR1, Ca-bound S100A1 intrudes deeper into the RyR1 structure beneath BSol than the apo-form and induces sideways motions of the C-terminal BSol region toward the adjacent RyR1 protomer resulting in tighter interprotomer contacts. Interestingly, the second hydrophobic pocket of the S100A1-dimer is largely exposed at the hydrophilic surface making it prone to interactions with the local environment, suggesting that S100A1 could be involved in forming larger heterocomplexes of RyRs with other protein partners. Since S100A1 interactions stabilizing BSol are implicated in the regulation of RyR-mediated Ca release, the characterization of the S100A1 binding site conserved between RyR isoforms may provide the structural basis for the development of therapeutic strategies regarding treatments of RyR-related disorders.
History
DepositionJan 8, 2024-
Header (metadata) releaseJan 17, 2024-
Map releaseJan 17, 2024-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43297.png

Downloads & links

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Map

FileDownload / File: emd_43297.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConstituent EM map: Focused refinement BSol/S100A1 of mouse RyR1 in complex with S100A1 (EGTA-only dataset)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 424.96 Å		0.83 Å/pix.
x 512 pix.
= 424.96 Å		0.83 Å/pix.
x 512 pix.
= 424.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.29176396 - 0.57267976
Average (Standard dev.)0.00025082118 (±0.017890168)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 424.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_43297_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_43297_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of RyR1 with Calstabin-1 and S100A1 (EGTA condition)

EntireName: Complex of RyR1 with Calstabin-1 and S100A1 (EGTA condition)
Components
  • Complex: Complex of RyR1 with Calstabin-1 and S100A1 (EGTA condition)

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Supramolecule #1: Complex of RyR1 with Calstabin-1 and S100A1 (EGTA condition)

SupramoleculeName: Complex of RyR1 with Calstabin-1 and S100A1 (EGTA condition)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Mus musculus (house mouse)

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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

Concentration8.5 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
10.0 mmol/LHEPES
150.0 mmol/Lsodium chlorideNaCl
0.25 %CHAPS
0.01 %DOPC
0.5 mmol/LTCEP
5.0 mmol/LEGTA
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details0.15 mmol/L S100A1-dimer

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 12147 / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL / In silico model: CryoSPARC ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 36506
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: CryoSPARC branch-and-bound
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: CryoSPARC branch-and-bound
FSC plot (resolution estimation)

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