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- EMDB-7781: Cardiac thin filament decorated with C0C1 fragment of cardiac myo... -

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Basic information

Entry
Database: EMDB / ID: 7781
TitleCardiac thin filament decorated with C0C1 fragment of cardiac myosin binding protein C mode 2
Map datacardiac thin filament decorated with C0C1 fragment of mysoin binding protein C
Samplecardiac thin filament decorated with C0C1 fragment of cardiac myosin binding protein C mode 2
  • actin
  • myosin binding protein C
  • tropomyosin
  • Actin, cytoplasmic 2
  • (Myosin-binding protein C, cardiac- ...) x 2
  • Tropomyosin
Function / homologyFibronectin type-III domain profile. / Immunoglobulin subtype / Formation of annular gap junctions / Immunoglobulin-like fold / Immunoglobulin I-set / Cell-extracellular matrix interactions / Immunoglobulin-like domain / Actin, conserved site / Actin family / Fibronectin type III ...Fibronectin type-III domain profile. / Immunoglobulin subtype / Formation of annular gap junctions / Immunoglobulin-like fold / Immunoglobulin I-set / Cell-extracellular matrix interactions / Immunoglobulin-like domain / Actin, conserved site / Actin family / Fibronectin type III / Interaction between L1 and Ankyrins / Fibronectin type III superfamily / VEGFA-VEGFR2 Pathway / Recycling pathway of L1 / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Immunoglobulin subtype 2 / Adherens junctions interactions / EPH-ephrin mediated repulsion of cells / EPHB-mediated forward signaling / Gap junction degradation / Striated Muscle Contraction / RHO GTPases activate IQGAPs / Actin/actin-like conserved site / Immunoglobulin-like domain superfamily / Actins signature 2. / Ig-like domain profile. / Actins and actin-related proteins signature. / Clathrin-mediated endocytosis / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling by BRAF and RAF fusions / Signaling by RAS mutants / Signaling by high-kinase activity BRAF mutants / Actin / Regulation of actin dynamics for phagocytic cup formation / Signaling by moderate kinase activity BRAF mutants / MAP2K and MAPK activation / Actins signature 1. / Immunoglobulin I-set domain / RHO GTPases Activate Formins / Fibronectin type III domain / RHO GTPases Activate WASPs and WAVEs / C zone / regulation of muscle filament sliding / striated muscle myosin thick filament / dense body / striated muscle myosin thick filament assembly / cardiac myofibril / profilin binding / structural molecule activity conferring elasticity / regulation of striated muscle contraction / calyx of Held / A band / positive regulation of ATPase activity / muscle alpha-actinin binding / ATPase activator activity / striated muscle contraction / cell junction assembly / muscle filament sliding / sarcomere organization / synaptic vesicle endocytosis / myosin binding / structural constituent of muscle / myofibril / M band / myosin heavy chain binding / ventricular cardiac muscle tissue morphogenesis / filamentous actin / heart morphogenesis / cardiac muscle contraction / phagocytic vesicle / sarcomere / titin binding / actin filament organization / Schaffer collateral - CA1 synapse / actin filament / structural constituent of cytoskeleton / cellular response to interferon-gamma / platelet aggregation / Z disc / ephrin receptor signaling pathway / actin filament binding / Fc-gamma receptor signaling pathway involved in phagocytosis / membrane organization / retina homeostasis / cytoskeleton / blood microparticle / cell adhesion / myelin sheath / ubiquitin protein ligase binding / focal adhesion / membrane / extracellular space / extracellular exosome / ATP binding / identical protein binding / plasma membrane / nucleus / metal ion binding / cytosol / Actin, cytoplasmic 2
Function and homology information
SourceHomo sapiens (human)
Methodhelical reconstruction / cryo EM / 11 Å resolution
AuthorsGalkin VE / Schroeder GF
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.
Validation ReportPDB-ID: 6cxj

SummaryFull reportAbout validation report
DateDeposition: Apr 3, 2018 / Header (metadata) release: May 30, 2018 / Map release: Oct 10, 2018 / Last update: Oct 10, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4237
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 4237
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6cxj
  • Surface level: 4237
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6cxj
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7781.map.gz (map file in CCP4 format, 8001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
2.1 Å/pix.
= 420. Å
100 pix
2.1 Å/pix.
= 210. Å
100 pix
2.1 Å/pix.
= 210. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.1 Å
Density
Contour Level:4237.0 (by author), 4237 (movie #1):
Minimum - Maximum-7231.725999999999658 - 12597.200000000000728
Average (Standard dev.)147.94144 (2070.887200000000121)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions100100200
Origin-50.0-50.0-99.0
Limit49.049.0100.0
Spacing100100200
CellA: 209.99998 Å / B: 209.99998 Å / C: 419.99997 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.12.12.1
M x/y/z100100200
origin x/y/z0.0000.0000.000
length x/y/z210.000210.000420.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-50-50-99
NC/NR/NS100100200
D min/max/mean-7231.72612597.200147.941

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Supplemental data

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Sample components

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Entire cardiac thin filament decorated with C0C1 fragment of cardiac myo...

EntireName: cardiac thin filament decorated with C0C1 fragment of cardiac myosin binding protein C mode 2
Number of components: 8

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Component #1: cellular-component, cardiac thin filament decorated with C0C1 fra...

Cellular-componentName: cardiac thin filament decorated with C0C1 fragment of cardiac myosin binding protein C mode 2
Recombinant expression: No

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Component #2: protein, actin

ProteinName: actin / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, myosin binding protein C

ProteinName: myosin binding protein C / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: protein, tropomyosin

ProteinName: tropomyosin / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, Actin, cytoplasmic 2

ProteinName: Actin, cytoplasmic 2 / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 41.792383 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #6: protein, Myosin-binding protein C, cardiac-type

ProteinName: Myosin-binding protein C, cardiac-type / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 12.164681 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #7: protein, Myosin-binding protein C, cardiac-type

ProteinName: Myosin-binding protein C, cardiac-type / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 10.688926 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #8: protein, Tropomyosin

ProteinName: Tropomyosin / Details: model / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 10.826337 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: helical array / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 27.5 Å / Delta phi: -166.6 deg.
Sample solutionpH: 7
VitrificationCryogen name: ETHANE / Temperature: 294 K / Humidity: 95 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionAlgorithm: BACK PROJECTION / Software: SPIDER / Resolution: 11 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Target criteria: Correlation coefficient / Refinement space: REAL
Output model

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