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- PDB-6cxi: Cardiac thin filament decorated with C0C1 fragment of cardiac myo... -

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Basic information

Entry
Database: PDB / ID: 6cxi
TitleCardiac thin filament decorated with C0C1 fragment of cardiac myosin binding protein C mode 1
Components
  • (Myosin-binding protein C, cardiac-type) x 2
  • Actin, cytoplasmic 2
  • Tropomyosin
KeywordsMOTOR PROTEIN / myosin binding protein C
Function / homology
Function and homology information


basal body patch / C zone / regulation of muscle filament sliding / striated muscle myosin thick filament / tight junction assembly / A band / regulation of striated muscle contraction / cardiac myofibril / profilin binding / protein localization to bicellular tight junction ...basal body patch / C zone / regulation of muscle filament sliding / striated muscle myosin thick filament / tight junction assembly / A band / regulation of striated muscle contraction / cardiac myofibril / profilin binding / protein localization to bicellular tight junction / regulation of transepithelial transport / Formation of annular gap junctions / morphogenesis of a polarized epithelium / Formation of the dystrophin-glycoprotein complex (DGC) / structural constituent of postsynaptic actin cytoskeleton / Gap junction degradation / Cell-extracellular matrix interactions / dense body / regulation of stress fiber assembly / Striated Muscle Contraction / Adherens junctions interactions / M band / regulation of cardiac muscle cell contraction / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / structural constituent of muscle / sarcomere organization / Sensory processing of sound by inner hair cells of the cochlea / regulation of focal adhesion assembly / apical junction complex / positive regulation of wound healing / myosin heavy chain binding / ventricular cardiac muscle tissue morphogenesis / myosin binding / maintenance of blood-brain barrier / filamentous actin / NuA4 histone acetyltransferase complex / myofibril / Recycling pathway of L1 / ATPase activator activity / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / regulation of synaptic vesicle endocytosis / RHO GTPases activate IQGAPs / RHOBTB2 GTPase cycle / heart morphogenesis / cardiac muscle contraction / phagocytic vesicle / titin binding / EPHB-mediated forward signaling / axonogenesis / calyx of Held / sarcomere / Translocation of SLC2A4 (GLUT4) to the plasma membrane / FCGR3A-mediated phagocytosis / actin filament / cell motility / RHO GTPases Activate Formins / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / Regulation of actin dynamics for phagocytic cup formation / cellular response to type II interferon / structural constituent of cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / VEGFA-VEGFR2 Pathway / platelet aggregation / Schaffer collateral - CA1 synapse / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / cell-cell junction / Signaling by BRAF and RAF1 fusions / actin cytoskeleton / Clathrin-mediated endocytosis / actin binding / angiogenesis / blood microparticle / cytoskeleton / cell adhesion / hydrolase activity / positive regulation of cell migration / axon / focal adhesion / synapse / ubiquitin protein ligase binding / positive regulation of gene expression / protein kinase binding / extracellular space / extracellular exosome / ATP binding / metal ion binding / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. ...: / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / ATPase, nucleotide binding domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Actin, cytoplasmic 2 / Myosin-binding protein C, cardiac-type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 11 Å
AuthorsGalkin, V.E. / Schroeder, G.F.
Funding support United States, 1items
OrganizationGrant numberCountry
American Heart Association560851 United States
CitationJournal: Structure / Year: 2018
Title: N-Terminal Domains of Cardiac Myosin Binding Protein C Cooperatively Activate the Thin Filament.
Authors: Cristina Risi / Betty Belknap / Eva Forgacs-Lonart / Samantha P Harris / Gunnar F Schröder / Howard D White / Vitold E Galkin /
Abstract: Muscle contraction relies on interaction between myosin-based thick filaments and actin-based thin filaments. Myosin binding protein C (MyBP-C) is a key regulator of actomyosin interactions. Recent ...Muscle contraction relies on interaction between myosin-based thick filaments and actin-based thin filaments. Myosin binding protein C (MyBP-C) is a key regulator of actomyosin interactions. Recent studies established that the N'-terminal domains (NTDs) of MyBP-C can either activate or inhibit thin filaments, but the mechanism of their collective action is poorly understood. Cardiac MyBP-C (cMyBP-C) harbors an extra NTD, which is absent in skeletal isoforms of MyBP-C, and its role in regulation of cardiac contraction is unknown. Here we show that the first two domains of human cMyPB-C (i.e., C0 and C1) cooperate to activate the thin filament. We demonstrate that C1 interacts with tropomyosin via a positively charged loop and that this interaction, stabilized by the C0 domain, is required for thin filament activation by cMyBP-C. Our data reveal a mechanism by which cMyBP-C can modulate cardiac contraction and demonstrate a function of the C0 domain.
History
DepositionApr 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first / _entity.formula_weight
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Actin, cytoplasmic 2
B: Actin, cytoplasmic 2
C: Actin, cytoplasmic 2
D: Actin, cytoplasmic 2
E: Actin, cytoplasmic 2
G: Myosin-binding protein C, cardiac-type
H: Myosin-binding protein C, cardiac-type
I: Myosin-binding protein C, cardiac-type
J: Myosin-binding protein C, cardiac-type
K: Myosin-binding protein C, cardiac-type
L: Myosin-binding protein C, cardiac-type
M: Myosin-binding protein C, cardiac-type
N: Myosin-binding protein C, cardiac-type
O: Myosin-binding protein C, cardiac-type
P: Myosin-binding protein C, cardiac-type
Q: Myosin-binding protein C, cardiac-type
S: Tropomyosin
T: Tropomyosin
U: Tropomyosin
V: Tropomyosin


Theoretical massNumber of molelcules
Total (without water)379,11420
Polymers379,11420
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area24010 Å2
ΔGint-160 kcal/mol
Surface area172940 Å2

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Components

#1: Protein
Actin, cytoplasmic 2 / Gamma-actin


Mass: 41838.766 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTG1, ACTG / Production host: Homo sapiens (human) / References: UniProt: P63261
#2: Protein
Myosin-binding protein C, cardiac-type / Cardiac MyBP-C / C-protein / cardiac muscle isoform


Mass: 12180.806 Da / Num. of mol.: 6 / Fragment: C1 Ig-domain (UNP residues 151-258)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYBPC3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14896
#3: Protein
Myosin-binding protein C, cardiac-type / Cardiac MyBP-C / C-protein / cardiac muscle isoform


Mass: 10706.060 Da / Num. of mol.: 5 / Fragment: C0 Ig-domain (UNP residues 1-101)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYBPC3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14896
#4: Protein
Tropomyosin


Mass: 10826.337 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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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

Component
IDNameTypeEntity IDParent-IDSourceDetails
1cardiac thin filament decorated with C0C1 fragment of cardiac myosin binding protein C mode 1ORGANELLE OR CELLULAR COMPONENTall0MULTIPLE SOURCES
2actinCOMPLEX#11RECOMBINANT
3myosin binding protein CCOMPLEX#2-#31RECOMBINANT
4tropomyosinCOMPLEX#41RECOMBINANTmodel
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Homo sapiens (human)9606
34Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Escherichia coli (E. coli)562
34Homo sapiens (human)9606
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in.
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 294 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 FIELD
Image recordingElectron dose: 20 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameCategoryDetails
2EPUimage acquisition
4CTFFINDCTF correction
7DireXmodel fitting
9CNSmodel refinement
10SPIDERinitial Euler assignment
11SPIDERfinal Euler assignment
12SPIDERclassification
13SPIDER3D reconstructionIHRSR
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -166.6 ° / Axial rise/subunit: 27.5 Å / Axial symmetry: C1
3D reconstructionResolution: 11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6117 / Algorithm: BACK PROJECTION / Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient

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