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- PDB-8v01: The structure of the native cardiac thin filament troponin core i... -

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Basic information

Entry
Database: PDB / ID: 8v01
TitleThe structure of the native cardiac thin filament troponin core in Ca2+-bound fully activated state 1 from the lower strand
Components
  • Actin, alpha cardiac muscle 1
  • Tropomyosin alpha-1 chain
  • Troponin C, slow skeletal and cardiac muscles
  • Troponin I, cardiac muscle
  • Troponin T2, cardiac type
KeywordsMOTOR PROTEIN / thin filament / troponin / tropomyosin / cryo-EM / muscle structure
Function / homology
Function and homology information


RHOB GTPase cycle / Striated Muscle Contraction / RHOA GTPase cycle / regulation of muscle filament sliding speed / troponin T binding / actin-myosin filament sliding / cardiac Troponin complex / troponin complex / regulation of muscle contraction / transition between fast and slow fiber ...RHOB GTPase cycle / Striated Muscle Contraction / RHOA GTPase cycle / regulation of muscle filament sliding speed / troponin T binding / actin-myosin filament sliding / cardiac Troponin complex / troponin complex / regulation of muscle contraction / transition between fast and slow fiber / ventricular cardiac muscle tissue morphogenesis / myosin binding / heart contraction / mesenchyme migration / troponin I binding / skeletal muscle contraction / cardiac muscle contraction / sarcomere / filopodium / actin filament organization / actin filament / calcium-dependent protein binding / actin filament binding / actin cytoskeleton / lamellipodium / cell body / actin binding / protein heterodimerization activity / calcium ion binding / positive regulation of gene expression / protein homodimerization activity / identical protein binding / cytoplasm
Similarity search - Function
Troponin T / Troponin I residues 1-32 / Troponin I residues 1-32 / Tropomyosins signature. / Tropomyosin / Troponin / Troponin domain superfamily / Tropomyosin / Troponin / EF-hand domain pair ...Troponin T / Troponin I residues 1-32 / Troponin I residues 1-32 / Tropomyosins signature. / Tropomyosin / Troponin / Troponin domain superfamily / Tropomyosin / Troponin / EF-hand domain pair / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / EF-hand domain pair / EF-hand, calcium binding motif / ATPase, nucleotide binding domain / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Troponin I, cardiac muscle / Troponin T, cardiac muscle / Actin, alpha cardiac muscle 1 / Tropomyosin alpha-1 chain / Troponin C, slow skeletal and cardiac muscles
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.5 Å
AuthorsGalkin, V.E. / Risi, C.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL160966 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)1R01HL140925 United States
CitationJournal: J Mol Biol / Year: 2024
Title: Troponin Structural Dynamics in the Native Cardiac Thin Filament Revealed by Cryo Electron Microscopy.
Authors: Cristina M Risi / Betty Belknap / Jennifer Atherton / Isabella Leite Coscarella / Howard D White / P Bryant Chase / Jose R Pinto / Vitold E Galkin /
Abstract: Cardiac muscle contraction occurs due to repetitive interactions between myosin thick and actin thin filaments (TF) regulated by Ca levels, active cross-bridges, and cardiac myosin-binding protein C ...Cardiac muscle contraction occurs due to repetitive interactions between myosin thick and actin thin filaments (TF) regulated by Ca levels, active cross-bridges, and cardiac myosin-binding protein C (cMyBP-C). The cardiac TF (cTF) has two nonequivalent strands, each comprised of actin, tropomyosin (Tm), and troponin (Tn). Tn shifts Tm away from myosin-binding sites on actin at elevated Ca levels to allow formation of force-producing actomyosin cross-bridges. The Tn complex is comprised of three distinct polypeptides - Ca-binding TnC, inhibitory TnI, and Tm-binding TnT. The molecular mechanism of their collective action is unresolved due to lack of comprehensive structural information on Tn region of cTF. C1 domain of cMyBP-C activates cTF in the absence of Ca to the same extent as rigor myosin. Here we used cryo-EM of native cTFs to show that cTF Tn core adopts multiple structural conformations at high and low Ca levels and that the two strands are structurally distinct. At high Ca levels, cTF is not entirely activated by Ca but exists in either partially or fully activated state. Complete dissociation of TnI C-terminus is required for full activation. In presence of cMyBP-C C1 domain, Tn core adopts a fully activated conformation, even in absence of Ca. Our data provide a structural description for the requirement of myosin to fully activate cTFs and explain increased affinity of TnC to Ca in presence of active cross-bridges. We suggest that allosteric coupling between Tn subunits and Tm is required to control actomyosin interactions.
History
DepositionNov 16, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actin, alpha cardiac muscle 1
B: Actin, alpha cardiac muscle 1
C: Troponin C, slow skeletal and cardiac muscles
D: Troponin I, cardiac muscle
E: Troponin T2, cardiac type
F: Tropomyosin alpha-1 chain
G: Tropomyosin alpha-1 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,14614
Polymers226,1237
Non-polymers1,0237
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 5 types, 7 molecules ABCDEFG

#1: Protein Actin, alpha cardiac muscle 1 / / Cardiac muscle alpha actin 1


Mass: 42064.891 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: B6VNT8
#2: Protein Troponin C, slow skeletal and cardiac muscles / / TN-C


Mass: 18433.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P63317
#3: Protein Troponin I, cardiac muscle / / Cardiac troponin I


Mass: 24092.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1V710
#4: Protein Troponin T2, cardiac type


Mass: 33941.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A5G2Q8N0
#5: Protein Tropomyosin alpha-1 chain / Alpha-tropomyosin / Tropomyosin-1


Mass: 32762.656 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P42639

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Non-polymers , 3 types, 7 molecules

#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: thin filament troponin core complex / Type: COMPLEX / Entity ID: #1-#5 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Sus scrofa (pig)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: non-helical filament
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: EMS Lacey Carbon
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K

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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 / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 34 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 24179

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Processing

EM software
IDNameVersionCategory
1RELION4particle selection
2EPUimage acquisition
4RELIONCTF correction
7PHENIXmodel fitting
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
11RELION4classification
12RELION43D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 8888787
3D reconstructionResolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 58709 / Details: Filtered to 7A / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
17KO5

7ko5

17KO51PDBexperimental model
27UTI

7uti

17UTI2PDBexperimental model
38DDO

8ddo
PDB Unreleased entry

18DDO3PDBexperimental model

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