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- PDB-5nog: Ca2+-induced Movement of Tropomyosin on Native Cardiac Thin Filam... -

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Basic information

Entry
Database: PDB / ID: 5nog
TitleCa2+-induced Movement of Tropomyosin on Native Cardiac Thin Filaments - "Blocked" state
Components
  • Cardiac muscle alpha actin 1
  • cardiac alpha tropomyosin
KeywordsMOTOR PROTEIN / F-actin / tropomyosin
Function / homology
Function and homology information


RHOB GTPase cycle / Striated Muscle Contraction / RHOA GTPase cycle / actin-myosin filament sliding / myosin binding / mesenchyme migration / heart contraction / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle fiber development ...RHOB GTPase cycle / Striated Muscle Contraction / RHOA GTPase cycle / actin-myosin filament sliding / myosin binding / mesenchyme migration / heart contraction / 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
ADENOSINE-5'-DIPHOSPHATE / Actin, alpha cardiac muscle 1 / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 11 Å
AuthorsRisi, C. / Eisner, J. / Belknap, B. / Heeley, D.H. / White, H.D. / Schroeder, G.F. / Galkin, V.E.
Funding support United States, 1items
OrganizationGrant numberCountry
AHAAid 560851 United States
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, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Data collection / Refinement description / Category: em_3d_fitting / em_image_scans / Item: _em_3d_fitting.target_criteria

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Assembly

Deposited unit
A: Cardiac muscle alpha actin 1
B: Cardiac muscle alpha actin 1
C: Cardiac muscle alpha actin 1
D: Cardiac muscle alpha actin 1
E: Cardiac muscle alpha actin 1
F: cardiac alpha tropomyosin
G: cardiac alpha tropomyosin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,36417
Polymers227,1077
Non-polymers2,25810
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area20720 Å2
ΔGint-199 kcal/mol
Surface area92240 Å2
MethodPISA

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Components

#1: Protein
Cardiac muscle alpha actin 1


Mass: 40818.477 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: B6VNT8, UniProt: P68137*PLUS
#2: Protein cardiac alpha tropomyosin


Mass: 11507.176 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Native Cardiac Thin Filaments / Type: ORGANELLE OR CELLULAR COMPONENT / Details: Sample contains actin, tropomyosin, and troponin. / Entity ID: #1-#2 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Sus scrofa (pig)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 30 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
4CTFFIND3CTF correction
7DIREXmodel fitting
13SPIDER3D reconstructionIHRSR
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 166.8 ° / Axial rise/subunit: 27.7 Å / Axial symmetry: C1
3D reconstructionResolution: 11 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 3809 / Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Details: Rigid fitting was done with Chimera and then DireX was used for flexible fitting.

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