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- EMDB-4346: human cardiac myosin binding protein C C1 Ig-domain bound to nati... -

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Basic information

Entry
Database: EMDB / ID: EMD-4346
Titlehuman cardiac myosin binding protein C C1 Ig-domain bound to native cardiac thin filament
Map data
Sample
  • Complex: human cardiac myosin binding protein C C1 Ig-domain bound to native cardiac thin filament
    • Complex: Actin, cytoplasmic 2
      • Protein or peptide: Actin, cytoplasmic 2
    • Complex: Myosin-binding protein C, cardiac-type
      • Protein or peptide: Myosin-binding protein C, cardiac-type
    • Complex: Tropomyosin
      • Protein or peptide: Tropomyosin
KeywordsCardiac thin filament regulator / CONTRACTILE PROTEIN
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) / Sus scrofa (pig)
Methodhelical reconstruction / cryo EM / Resolution: 9.0 Å
AuthorsRisi C / Belknap B
Funding support United States, 1 items
OrganizationGrant numberCountry
American Heart Association16GRNT31220040 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
DepositionMar 23, 2018-
Header (metadata) releaseMay 23, 2018-
Map releaseOct 17, 2018-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5964
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 5964
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6g2t
  • Surface level: 5964
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6g2t
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4346.png

Downloads & links

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Map

FileDownload / File: emd_4346.map.gz / Format: CCP4 / Size: 5.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.1 Å/pix.
x 150 pix.
= 315. 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: 5964.0 / Movie #1: 5964
Minimum - Maximum-8901.734000000000378 - 20462.427999999999884
Average (Standard dev.)501.144900000000007 (±2122.063999999999851)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-74
Dimensions100100150
Spacing100100150
CellA: 209.99998 Å / B: 209.99998 Å / C: 315.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.12.12.1
M x/y/z100100150
origin x/y/z0.0000.0000.000
length x/y/z210.000210.000315.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS-50-50-74
NC/NR/NS100100150
D min/max/mean-8901.73420462.428501.145

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Supplemental data

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Sample components

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Entire : human cardiac myosin binding protein C C1 Ig-domain bound to nati...

EntireName: human cardiac myosin binding protein C C1 Ig-domain bound to native cardiac thin filament
Components
  • Complex: human cardiac myosin binding protein C C1 Ig-domain bound to native cardiac thin filament
    • Complex: Actin, cytoplasmic 2
      • Protein or peptide: Actin, cytoplasmic 2
    • Complex: Myosin-binding protein C, cardiac-type
      • Protein or peptide: Myosin-binding protein C, cardiac-type
    • Complex: Tropomyosin
      • Protein or peptide: Tropomyosin

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Supramolecule #1: human cardiac myosin binding protein C C1 Ig-domain bound to nati...

SupramoleculeName: human cardiac myosin binding protein C C1 Ig-domain bound to native cardiac thin filament
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Sample contains actin, tropomyosin, troponin complex, myosin binding protein-C C0-C1 Ig domains. Only C1 Ig-domain bound to the cardiac thin filament is visualized in the map

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Supramolecule #2: Actin, cytoplasmic 2

SupramoleculeName: Actin, cytoplasmic 2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Myosin-binding protein C, cardiac-type

SupramoleculeName: Myosin-binding protein C, cardiac-type / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: Tropomyosin

SupramoleculeName: Tropomyosin / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Sus scrofa (pig)

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Macromolecule #1: Actin, cytoplasmic 2

MacromoleculeName: Actin, cytoplasmic 2 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.838766 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEEEIAALVI DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSGDGV T HTVPIYEG ...String:
MEEEIAALVI DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSGDGV T HTVPIYEG YALPHAILRL DLAGRDLTDY LMKILTERGY SFTTTAEREI VRDIKEKLCY VALDFEQEMA TAASSSSLEK SY ELPDGQV ITIGNERFRC PEALFQPSFL GMESCGIHET TFNSIMKCDV DIRKDLYANT VLSGGTTMYP GIADRMQKEI TAL APSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ISKQEYDESG PSIVHRKCF

UniProtKB: Actin, cytoplasmic 2

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Macromolecule #2: Myosin-binding protein C, cardiac-type

MacromoleculeName: Myosin-binding protein C, cardiac-type / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.180806 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MDDPIGLFVM RPQDGEVTVG GSITFSARVA GASLLKPPVV KWFKGKWVDL SSKVGQHLQL HDSYDRASKV YLFELHITDA QPAFTGSYR CEVSTKDKFD CSNFNLTVHE

UniProtKB: Myosin-binding protein C, cardiac-type

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Macromolecule #3: Tropomyosin

MacromoleculeName: Tropomyosin / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (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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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7
GridMaterial: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 294 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 20.0 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: -166.6 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPIDER / Software - details: IHRSR / Number images used: 7051
Startup modelType of model: OTHER / Details: cylinder density map
Final angle assignmentType: NOT APPLICABLE / Software - Name: SPIDER / Software - details: IHRSR

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-6g2t:
human cardiac myosin binding protein C C1 Ig-domain bound to native cardiac thin filament

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