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- EMDB-1909: Skeletal thick filament showing myosin crowns and MyBP-C -

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Basic information

Entry
Database: EMDB / ID: EMD-1909
TitleSkeletal thick filament showing myosin crowns and MyBP-C
Map dataAveraged thick filament tomogram showing myosin crowns and MyBP-C
Sample
  • Sample: Thin section of fast-frozen/freeze substituted relaxed frog sartorius muscle.
  • Organelle or cellular component: Thick filament
KeywordsC-protein / myosin binding protein C / electron tomography / thick filament structure
Biological speciesAnura (frogs & toads)
Methodsubtomogram averaging / cryo EM / Resolution: 70.0 Å
AuthorsLuther PK / Winkler H / Taylor K / Zoghbi ME / Craig R / Padron R / Squire JM / Liu J
CitationJournal: Proc Natl Acad Sci U S A / Year: 2011
Title: Direct visualization of myosin-binding protein C bridging myosin and actin filaments in intact muscle.
Authors: Pradeep K Luther / Hanspeter Winkler / Kenneth Taylor / Maria E Zoghbi / Roger Craig / Raúl Padrón / John M Squire / Jun Liu /
Abstract: Myosin-binding protein C (MyBP-C) is a thick filament protein playing an essential role in muscle contraction, and MyBP-C mutations cause heart and skeletal muscle disease in millions worldwide. ...Myosin-binding protein C (MyBP-C) is a thick filament protein playing an essential role in muscle contraction, and MyBP-C mutations cause heart and skeletal muscle disease in millions worldwide. Despite its discovery 40 y ago, the mechanism of MyBP-C function remains unknown. In vitro studies suggest that MyBP-C could regulate contraction in a unique way--by bridging thick and thin filaments--but there has been no evidence for this in vivo. Here we use electron tomography of exceptionally well preserved muscle to demonstrate that MyBP-C does indeed bind to actin in intact muscle. This binding implies a physical mechanism for communicating the relative sliding between thick and thin filaments that does not involve myosin and which could modulate the contractile process.
History
DepositionJun 10, 2011-
Header (metadata) releaseSep 26, 2012-
Map releaseSep 26, 2012-
UpdateOct 10, 2012-
Current statusOct 10, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.33
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.33
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-1909.png

Downloads & links

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Map

FileDownload / File: emd_1909.map.gz / Format: CCP4 / Size: 13.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAveraged thick filament tomogram showing myosin crowns and MyBP-C
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
11.5 Å/pix.
x 560 pix.
= 6440. Å		11.5 Å/pix.
x 80 pix.
= 920. Å		11.5 Å/pix.
x 80 pix.
= 920. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 11.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.33 / Movie #1: 0.33
Minimum - Maximum-0.94029731 - 0.81897604
Average (Standard dev.)0.01339361 (±0.14325161)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions8080560
Spacing8080560
CellA: 920.0 Å / B: 920.0 Å / C: 6440.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z11.511.511.5
M x/y/z8080560
origin x/y/z0.0000.0000.000
length x/y/z920.000920.0006440.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS8080560
D min/max/mean-0.9400.8190.013

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Supplemental data

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Sample components

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Entire : Thin section of fast-frozen/freeze substituted relaxed frog sarto...

EntireName: Thin section of fast-frozen/freeze substituted relaxed frog sartorius muscle.
Components
  • Sample: Thin section of fast-frozen/freeze substituted relaxed frog sartorius muscle.
  • Organelle or cellular component: Thick filament

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Supramolecule #1000: Thin section of fast-frozen/freeze substituted relaxed frog sarto...

SupramoleculeName: Thin section of fast-frozen/freeze substituted relaxed frog sartorius muscle.
type: sample / ID: 1000 / Number unique components: 1
Molecular weightExperimental: 130 KDa / Theoretical: 130 KDa

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Supramolecule #1: Thick filament

SupramoleculeName: Thick filament / type: organelle_or_cellular_component / ID: 1 / Name.synonym: Thick filament / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Anura (frogs & toads)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging

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Sample preparation

VitrificationCryogen name: HELIUM / Instrument: OTHER

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: Eucentric / Specimen holder model: OTHER

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Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 70.0 Å / Resolution method: OTHER / Software - Name: Protomo

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Atomic model buiding 1

Initial modelPDB ID:

1i84

RefinementSpace: REAL

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