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- EMDB-3665: Ca2+-induced Movement of Tropomyosin on Native Cardiac Thin Filam... -

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Basic information

Entry
Database: EMDB / ID: EMD-3665
TitleCa2+-induced Movement of Tropomyosin on Native Cardiac Thin Filaments - "Blocked" state
Map dataNative cardiac thin filament in S-blocked state.
Sample
  • Organelle or cellular component: Native Cardiac Thin Filaments
    • Protein or peptide: Cardiac muscle alpha actin 1
    • Protein or peptide: cardiac alpha tropomyosin
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
Function / homology
Function and homology information


Striated Muscle Contraction / actin-myosin filament sliding / myosin binding / heart contraction / mesenchyme migration / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle fiber development / stress fiber / sarcomere ...Striated Muscle Contraction / actin-myosin filament sliding / myosin binding / heart contraction / mesenchyme migration / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle fiber development / stress fiber / sarcomere / filopodium / actin filament organization / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / lamellipodium / cell body / hydrolase activity / positive regulation of gene expression / ATP binding / cytoplasm
Similarity search - Function
Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Actin, alpha cardiac muscle 1 / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesSus scrofa (pig) / Pig (pig)
Methodhelical reconstruction / cryo EM / Resolution: 11.0 Å
AuthorsRisi C / Eisner J / Belknap B / Heeley DH / White HD / Schroeder GF / Galkin VE
CitationJournal: Proc Natl Acad Sci U S A / Year: 2017
Title: Ca-induced movement of tropomyosin on native cardiac thin filaments revealed by cryoelectron microscopy.
Authors: Cristina Risi / Jamie Eisner / Betty Belknap / David H Heeley / Howard D White / Gunnar F Schröder / Vitold E Galkin /
Abstract: Muscle contraction relies on the interaction of myosin motors with F-actin, which is regulated through a translocation of tropomyosin by the troponin complex in response to Ca The current model of ...Muscle contraction relies on the interaction of myosin motors with F-actin, which is regulated through a translocation of tropomyosin by the troponin complex in response to Ca The current model of muscle regulation holds that at relaxing (low-Ca) conditions tropomyosin blocks myosin binding sites on F-actin, whereas at activating (high-Ca) conditions tropomyosin translocation only partially exposes myosin binding sites on F-actin so that binding of rigor myosin is required to fully activate the thin filament (TF). Here we used a single-particle approach to helical reconstruction of frozen hydrated native cardiac TFs under relaxing and activating conditions to reveal the azimuthal movement of the tropomyosin on the surface of the native cardiac TF upon Ca activation. We demonstrate that at either relaxing or activating conditions tropomyosin is not constrained in one structural state, but rather is distributed between three structural positions on the surface of the TF. We show that two of these tropomyosin positions restrain actomyosin interactions, whereas in the third position, which is significantly enhanced at high Ca, tropomyosin does not block myosin binding sites on F-actin. Our data provide a structural framework for the enhanced activation of the cardiac TF over the skeletal TF by Ca and lead to a mechanistic model for the regulation of the cardiac TF.
History
DepositionApr 12, 2017-
Header (metadata) releaseJul 19, 2017-
Map releaseJul 19, 2017-
UpdateAug 30, 2017-
Current statusAug 30, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 50
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 50
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5nog
  • Surface level: 50
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5nog
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3665.png

Downloads & links

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Map

FileDownload / File: emd_3665.map.gz / Format: CCP4 / Size: 8.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNative cardiac thin filament in S-blocked state.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.1 Å/pix.
x 230 pix.
= 483. Å		2.1 Å/pix.
x 100 pix.
= 210. Å		2.1 Å/pix.
x 100 pix.
= 210. 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: 2.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 50. / Movie #1: 50
Minimum - Maximum-75.894469999999998 - 154.499470000000002
Average (Standard dev.)4.1177936 (±17.356521999999998)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-114
Dimensions100100230
Spacing100100230
CellA: 209.99998 Å / B: 209.99998 Å / C: 482.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.12.12.1
M x/y/z100100230
origin x/y/z0.0000.0000.000
length x/y/z210.000210.000483.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-50-50-114
NC/NR/NS100100230
D min/max/mean-75.894154.4994.118

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Supplemental data

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Sample components

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Entire : Native Cardiac Thin Filaments

EntireName: Native Cardiac Thin Filaments
Components
  • Organelle or cellular component: Native Cardiac Thin Filaments
    • Protein or peptide: Cardiac muscle alpha actin 1
    • Protein or peptide: cardiac alpha tropomyosin
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Native Cardiac Thin Filaments

SupramoleculeName: Native Cardiac Thin Filaments / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: Sample contains actin, tropomyosin, and troponin.
Source (natural)Organism: Sus scrofa (pig)

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Macromolecule #1: Cardiac muscle alpha actin 1

MacromoleculeName: Cardiac muscle alpha actin 1 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Pig (pig)
Molecular weightTheoretical: 40.818477 KDa
SequenceString: TTALVCDNGS GLVKAGFAGD DAPRAVFPSI VGRPRHQGVM VGMGQKDSYV GDEAQSKRGI LTLKYPIE(HIC)G IITNWD DME KIWHHTFYNE LRVAPEEHPT LLTEAPLNPK ANREKMTQIM FETFNVPAMY VAIQAVLSLY ASGRTTGIVL DSGDGVT HN VPIYEGYALP ...String:
TTALVCDNGS GLVKAGFAGD DAPRAVFPSI VGRPRHQGVM VGMGQKDSYV GDEAQSKRGI LTLKYPIE(HIC)G IITNWD DME KIWHHTFYNE LRVAPEEHPT LLTEAPLNPK ANREKMTQIM FETFNVPAMY VAIQAVLSLY ASGRTTGIVL DSGDGVT HN VPIYEGYALP HAIMRLDLAG RDLTDYLMKI LTERGYSFVT TAEREIVRDI KEKLCYVALD FENEMATAAS SSSLEKSY E LPDGQVITIG NERFRCPETL FQPSFIGMES AGIHETTYNS IMKCDIDIRK DLYANNVLSG GTTMYPGIAD RMQKEITAL APSTMKIKII APPERKYSVW IGGSILASLS TFQQMWISKQ EYDEAGPSIV H

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Macromolecule #2: cardiac alpha tropomyosin

MacromoleculeName: cardiac alpha tropomyosin / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pig (pig)
Molecular weightTheoretical: 11.507176 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 5 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 27.7 Å
Applied symmetry - Helical parameters - Δ&Phi: 166.8 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 11.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Software - details: IHRSR / Number images used: 3809
CTF correctionSoftware - Name: CTFFIND (ver. 3)
Startup modelType of model: OTHER / Details: solid cylinder
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

DetailsRigid fitting was done with Chimera and then DireX was used for flexible fitting.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-5nog:
Ca2+-induced Movement of Tropomyosin on Native Cardiac Thin Filaments - "Blocked" state

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