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- EMDB-2240: 3D structure of myosin filaments isolated from human heart muscle... -

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Basic information

Entry
Database: EMDB / ID: EMD-2240
Title3D structure of myosin filaments isolated from human heart muscles by negative stain electron microscopy and single particle image analysis.
Map data3D map of human cardiac myosin filament
Sample
  • Sample: 3D map of human cardiac myosin filament
  • Protein or peptide: myosin filament
Keywordsmyosin filaments / human cardiac muscles / single particle analysis / electron microscopy / muscle contraction
Function / homology
Function and homology information


myosin II heavy chain binding / muscle cell fate specification / regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / cardiac myofibril / regulation of striated muscle contraction / cardiac myofibril assembly / muscle myosin complex / muscle filament sliding / regulation of the force of heart contraction ...myosin II heavy chain binding / muscle cell fate specification / regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / cardiac myofibril / regulation of striated muscle contraction / cardiac myofibril assembly / muscle myosin complex / muscle filament sliding / regulation of the force of heart contraction / transition between fast and slow fiber / myosin filament / adult heart development / positive regulation of ATP-dependent activity / Striated Muscle Contraction / cardiac muscle hypertrophy in response to stress / I band / A band / myosin II complex / myosin complex / structural constituent of muscle / ventricular cardiac muscle tissue morphogenesis / sarcomere organization / microfilament motor activity / heart contraction / myosin heavy chain binding / myofibril / positive regulation of the force of heart contraction / actin monomer binding / skeletal muscle contraction / ATP metabolic process / striated muscle contraction / stress fiber / cardiac muscle contraction / muscle contraction / regulation of heart rate / sarcomere / negative regulation of cell growth / Z disc / actin filament binding / heart development / cytoskeleton / calmodulin binding / calcium ion binding / ATP binding / cytosol / cytoplasm
Similarity search - Function
: / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site ...: / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / : / Kinesin motor domain superfamily / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Myosin light chain 3 / Myosin regulatory light chain 2, ventricular/cardiac muscle isoform / Myosin-7
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / Resolution: 28.0 Å
AuthorsAL-Khayat HA / Kensler RW / Squire JM / Marston SB / Morris EP
CitationJournal: Proc Natl Acad Sci U S A / Year: 2013
Title: Atomic model of the human cardiac muscle myosin filament.
Authors: Hind A Al-Khayat / Robert W Kensler / John M Squire / Steven B Marston / Edward P Morris /
Abstract: Of all the myosin filaments in muscle, the most important in terms of human health, and so far the least studied, are those in the human heart. Here we report a 3D single-particle analysis of ...Of all the myosin filaments in muscle, the most important in terms of human health, and so far the least studied, are those in the human heart. Here we report a 3D single-particle analysis of electron micrograph images of negatively stained myosin filaments isolated from human cardiac muscle in the normal (undiseased) relaxed state. The resulting 28-Å resolution 3D reconstruction shows axial and azimuthal (no radial) myosin head perturbations within the 429-Å axial repeat, with rotations between successive 132 Å-, 148 Å-, and 149 Å-spaced crowns of heads close to 60°, 35°, and 25° (all would be 40° in an unperturbed three-stranded helix). We have defined the myosin head atomic arrangements within the three crown levels and have modeled the organization of myosin subfragment 2 and the possible locations of the 39 Å-spaced domains of titin and the cardiac isoform of myosin-binding protein-C on the surface of the myosin filament backbone. Best fits were obtained with head conformations on all crowns close to the structure of the two-headed myosin molecule of vertebrate chicken smooth muscle in the dephosphorylated relaxed state. Individual crowns show differences in head-pair tilts and subfragment 2 orientations, which, together with the observed perturbations, result in different intercrown head interactions, including one not reported before. Analysis of the interactions between the myosin heads, the cardiac isoform of myosin-binding protein-C, and titin will aid in understanding of the structural effects of mutations in these proteins known to be associated with human cardiomyopathies.
History
DepositionDec 7, 2012-
Header (metadata) releaseDec 26, 2012-
Map releaseDec 26, 2012-
UpdateDec 26, 2012-
Current statusDec 26, 2012Processing site: PDBe / Status: Released

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Structure visualization

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  • Surface view with section colored by density value
  • Surface level: 1.5
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  • Surface view colored by cylindrical radius
  • Surface level: 1.5
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  • Surface view with fitted model
  • Atomic models: PDB-5tby
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5tby
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5tby
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2240.jpg

Downloads & links

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Map

FileDownload / File: emd_2240.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D map of human cardiac myosin filament
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.94 Å/pix.
x 160 pix.
= 950.4 Å		5.94 Å/pix.
x 160 pix.
= 950.4 Å		5.94 Å/pix.
x 160 pix.
= 950.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5 / Movie #1: 1.5
Minimum - Maximum-8.24266529 - 12.488184929999999
Average (Standard dev.)0.04301857 (±0.77574736)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-79-80-80
Dimensions160160160
Spacing160160160
CellA=B=C: 950.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.945.945.94
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z950.400950.400950.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-36-30-80
NX/NY/NZ7361161
MAP C/R/S123
start NC/NR/NS-80-79-80
NC/NR/NS160160160
D min/max/mean-8.24312.4880.043

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Supplemental data

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Sample components

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Entire : 3D map of human cardiac myosin filament

EntireName: 3D map of human cardiac myosin filament
Components
  • Sample: 3D map of human cardiac myosin filament
  • Protein or peptide: myosin filament

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Supramolecule #1000: 3D map of human cardiac myosin filament

SupramoleculeName: 3D map of human cardiac myosin filament / type: sample / ID: 1000 / Number unique components: 1

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Macromolecule #1: myosin filament

MacromoleculeName: myosin filament / type: protein_or_peptide / ID: 1 / Details: 3D map of human cardiac myosin filament / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Homo sapiens (human) / synonym: human

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Experimental details

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Structure determination

Processingsubtomogram averaging

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Sample preparation

VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI 20
DateMay 15, 2012
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Digitization - Sampling interval: 17 µm / Number real images: 237 / Average electron dose: 100 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: OTHER / Nominal magnification: 29000
Sample stageSpecimen holder model: OTHER

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Image processing

DetailsAverage number of tilts used in the 3D reconstructions: 285.
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: OTHER / Software - Name: imagic

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Atomic model buiding 1

Initial modelPDB ID:

1myo

SoftwareName: pymol and veda
DetailsProtocol: rigid body
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-5tby:
HUMAN BETA CARDIAC HEAVY MEROMYOSIN INTERACTING-HEADS MOTIF OBTAINED BY HOMOLOGY MODELING (USING SWISS-MODEL) OF HUMAN SEQUENCE FROM APHONOPELMA HOMOLOGY MODEL (PDB-3JBH), RIGIDLY FITTED TO HUMAN BETA-CARDIAC NEGATIVELY STAINED THICK FILAMENT 3D-RECONSTRUCTION (EMD-2240)

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