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- EMDB-7029: CryoEM map from poorly ordered myosin thick filaments isolated fr... -

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Basic information

Entry
Database: EMDB / ID: EMD-7029
TitleCryoEM map from poorly ordered myosin thick filaments isolated from asynchronous flight muscle of the large waterbug Lethocerus indicus
Map dataPrimary map
Sample
  • Complex: Lethocerus flight muscle myosin filament
Biological speciesLethocerus indicus (insect)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.4 Å
AuthorsTaylor KA / Taylor D / Hu Z / Edwards RJ
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM030598 United States
American Heart Association15PRE25090150 United States
NIH/NIAMSR01 AR014317 United States
NIH/Office of the DirectorS10 OD018142 United States
NIH/NCRRS10 RR25080 United States
CitationJournal: J Struct Biol / Year: 2017
Title: Coupling between myosin head conformation and the thick filament backbone structure.
Authors: Zhongjun Hu / Dianne W Taylor / Robert J Edwards / Kenneth A Taylor /
Abstract: The recent high-resolution structure of the thick filament from Lethocerus asynchronous flight muscle shows aspects of thick filament structure never before revealed that may shed some light on how ...The recent high-resolution structure of the thick filament from Lethocerus asynchronous flight muscle shows aspects of thick filament structure never before revealed that may shed some light on how striated muscles function. The phenomenon of stretch activation underlies the function of asynchronous flight muscle. It is most highly developed in flight muscle, but is also observed in other striated muscles such as cardiac muscle. Although stretch activation is likely to be complex, involving more than a single structural aspect of striated muscle, the thick filament itself, would be a prime site for regulatory function because it must bear all of the tension produced by both its associated myosin motors and any externally applied force. Here we show the first structural evidence that the arrangement of myosin heads within the interacting heads motif is coupled to the structure of the thick filament backbone. We find that a change in helical angle of 0.16° disorders the blocked head preferentially within the Lethocerus interacting heads motif. This observation suggests a mechanism for how tension affects the dynamics of the myosin heads leading to a detailed hypothesis for stretch activation and shortening deactivation, in which the blocked head preferentially binds the thin filament followed by the free head when force production occurs.
History
DepositionSep 15, 2017-
Header (metadata) releaseOct 11, 2017-
Map releaseOct 11, 2017-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6so3
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7029.png

Downloads & links

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Map

FileDownload / File: emd_7029.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary map
Voxel sizeX=Y=Z: 1.223 Å
Density
Contour LevelBy AUTHOR: 0.032 / Movie #1: 0.012
Minimum - Maximum-0.056497645 - 0.18061732
Average (Standard dev.)0.00056291226 (±0.009138624)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 528.336 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2231.2231.223
M x/y/z432432432
origin x/y/z0.0000.0000.000
length x/y/z528.336528.336528.336
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS432432432
D min/max/mean-0.0560.1810.001

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Supplemental data

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Sample components

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Entire : Lethocerus flight muscle myosin filament

EntireName: Lethocerus flight muscle myosin filament
Components
  • Complex: Lethocerus flight muscle myosin filament

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Supramolecule #1: Lethocerus flight muscle myosin filament

SupramoleculeName: Lethocerus flight muscle myosin filament / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Lethocerus indicus (insect) / Organ: Dorsal longitudinal flight muscle / Tissue: striated muscle / Organelle: myofibril

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 6.8
GridModel: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER / Details: Gatan Solarus 950.M plasma cleaner
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV
DetailsAll specimen and sample preparation details may be found in Z. Hu, D. W. Taylor, M. K. Reedy, R. J. Edwards, K. A. Taylor, Structure of myosin filaments from relaxed Lethocerus flight muscle by cryo-EM at 6 Angstrom resolution. Sci. Adv. 2, e1600058 (2016). Can also be found in the Specimen section of EMD-3301

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
DetailsAll data collection details may be found in Z. Hu, D. W. Taylor, M. K. Reedy, R. J. Edwards, K. A. Taylor, Structure of myosin filaments from relaxed Lethocerus flight muscle by cryo-EM at 6 Angstrom resolution. Sci. Adv. 2, e1600058 (2016). Can also be found in the Specimen section of EMD-3301
Image recordingFilm or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Detector mode: INTEGRATING / Digitization - Frames/image: 1-48 / Average exposure time: 1.5 sec. / Average electron dose: 65.0 e/Å2
Details: All specimen and sample preparation details may be found in Z. Hu, D. W. Taylor, M. K. Reedy, R. J. Edwards, K. A. Taylor, Structure of myosin filaments from relaxed Lethocerus flight muscle ...Details: All specimen and sample preparation details may be found in Z. Hu, D. W. Taylor, M. K. Reedy, R. J. Edwards, K. A. Taylor, Structure of myosin filaments from relaxed Lethocerus flight muscle by cryo-EM at 6 Angstrom resolution. Sci. Adv. 2, e1600058 (2016). Can also be found in the Specimen section of EMD-3301
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 100000
Details: All specimen and sample preparation details may be found in Z. Hu, D. W. Taylor, M. K. Reedy, R. J. Edwards, K. A. Taylor, Structure of myosin filaments from relaxed Lethocerus flight muscle ...Details: All specimen and sample preparation details may be found in Z. Hu, D. W. Taylor, M. K. Reedy, R. J. Edwards, K. A. Taylor, Structure of myosin filaments from relaxed Lethocerus flight muscle by cryo-EM at 6 Angstrom resolution. Sci. Adv. 2, e1600058 (2016). Can also be found in the Specimen section of EMD-3301
CTF correctionSoftware - Name: ACE, CTFFIND3
Details: All specimen and sample preparation details may be found in Z. Hu, D. W. Taylor, M. K. Reedy, R. J. Edwards, K. A. Taylor, Structure of myosin filaments from relaxed Lethocerus flight muscle ...Details: All specimen and sample preparation details may be found in Z. Hu, D. W. Taylor, M. K. Reedy, R. J. Edwards, K. A. Taylor, Structure of myosin filaments from relaxed Lethocerus flight muscle by cryo-EM at 6 Angstrom resolution. Sci. Adv. 2, e1600058 (2016). Can also be found in the Specimen section of EMD-3301
Startup modelType of model: OTHER / Details: Map from EMD-3301 low pass filtered to 60 angstrom
Initial angle assignmentType: NOT APPLICABLE / Software - Name: EMAN
Software - details: STARTCSYM routine, which uses the common line method
Final 3D classificationNumber classes: 4 / Avg.num./class: 25000
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.2)
Software - details: IHRSR implementation by Clemens et al., Cell 160, 940?951 (2015).
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.2)
Software - details: IHRSR implementation by Clemens et al., Cell 160, 940?951 (2015).
Number images used: 50000
DetailsAll specimen and sample preparation details may be found in Z. Hu, D. W. Taylor, M. K. Reedy, R. J. Edwards, K. A. Taylor, Structure of myosin filaments from relaxed Lethocerus flight muscle by cryo-EM at 6 Angstrom resolution. Sci. Adv. 2, e1600058 (2016). Can also be found in the Specimen section of EMD-3301
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-6so3:
The interacting head motif in insect flight muscle myosin thick filaments

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