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- EMDB-23497: Filamentous actin decorated with human cardiac myosin binding pro... -

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Basic information

Entry
Database: EMDB / ID: EMD-23497
TitleFilamentous actin decorated with human cardiac myosin binding protein C C2 domain
Map dataFilamentous actin decorated with human cardiac myosin binding protein C C2 domain
Sample
  • Complex: Filamentous actin decorated with human cardiac myosin binding protein C C2 domain
    • Complex: Filamentous actin
      • Protein or peptide: Actin, alpha cardiac muscle 1
    • Complex: Cardiac myosin binding protein C C2 domain
      • Protein or peptide: Myosin-binding protein C, cardiac-type
Keywordsmyosin binding protein C / actin / thin filament / MOTOR PROTEIN
Function / homology
Function and homology information


C zone / regulation of muscle filament sliding / striated muscle myosin thick filament / cardiac myofibril / actin-myosin filament sliding / regulation of striated muscle contraction / positive regulation of ATP-dependent activity / Striated Muscle Contraction / ventricular cardiac muscle tissue morphogenesis / A band ...C zone / regulation of muscle filament sliding / striated muscle myosin thick filament / cardiac myofibril / actin-myosin filament sliding / regulation of striated muscle contraction / positive regulation of ATP-dependent activity / Striated Muscle Contraction / ventricular cardiac muscle tissue morphogenesis / A band / structural constituent of muscle / sarcomere organization / myosin binding / heart contraction / myosin heavy chain binding / mesenchyme migration / ATPase activator activity / heart morphogenesis / cardiac muscle contraction / titin binding / sarcomere / filopodium / actin filament organization / actin filament / lamellipodium / actin binding / cell body / cell adhesion / positive regulation of gene expression / identical protein binding / metal ion binding / cytosol / cytoplasm
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, alpha cardiac muscle 1 / Myosin-binding protein C, cardiac-type
Similarity search - Component
Biological speciesSus scrofa (pig) / Homo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 6.1 Å
AuthorsGalkin VE
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL140925 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116790 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116788 United States
CitationJournal: J Mol Biol / Year: 2021
Title: Interaction of the C2 Ig-like Domain of Cardiac Myosin Binding Protein-C with F-actin.
Authors: Cristina M Risi / Malay Patra / Betty Belknap / Samantha P Harris / Howard D White / Vitold E Galkin /
Abstract: Cardiac muscle contraction depends on interactions between thick (myosin) and thin (actin) filaments (TFs). TFs are regulated by intracellular Ca levels. Under activating conditions Ca binds to the ...Cardiac muscle contraction depends on interactions between thick (myosin) and thin (actin) filaments (TFs). TFs are regulated by intracellular Ca levels. Under activating conditions Ca binds to the troponin complex and displaces tropomyosin from myosin binding sites on the TF surface to allow actomyosin interactions. Recent studies have shown that in addition to Ca, the first four N-terminal domains (NTDs) of cardiac myosin binding protein C (cMyBP-C) (e.g. C0, C1, M and C2), are potent modulators of the TF activity, but the mechanism of their collective action is poorly understood. Previously, we showed that C1 activates the TF at low Ca and C0 stabilizes binding of C1 to the TF, but the ability of C2 to bind and/or affect the TF remains unknown. Here we obtained 7.5 Å resolution cryo-EM reconstruction of C2-decorated actin filaments to demonstrate that C2 binds to actin in a single structural mode that does not activate the TF unlike the polymorphic binding of C0 and C1 to actin. Comparison of amino acid sequences of C2 with either C0 or C1 shows low levels of identity between the residues involved in interactions with the TF but high levels of conservation for residues involved in Ig fold stabilization. This provides a structural basis for strikingly different interactions of structurally homologous C0, C1 and C2 with the TF. Our detailed analysis of the interaction of C2 with the actin filament provides crucial information required to model the collective action of cMyBP-C NTDs on the cardiac TF.
History
DepositionFeb 16, 2021-
Header (metadata) releaseAug 11, 2021-
Map releaseAug 11, 2021-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.75
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.75
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7lrg
  • Surface level: 0.75
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23497.png

Downloads & links

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Map

FileDownload / File: emd_23497.map.gz / Format: CCP4 / Size: 11.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFilamentous actin decorated with human cardiac myosin binding protein C C2 domain
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 110 pix.
= 118.8 Å		1.08 Å/pix.
x 108 pix.
= 116.64 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: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.75 / Movie #1: 0.75
Minimum - Maximum-3.5856218 - 11.2547245
Average (Standard dev.)-0.000000000016836 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions110108256
Spacing108110256
CellA: 116.64001 Å / B: 118.8 Å / C: 276.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z108110256
origin x/y/z0.0000.0000.000
length x/y/z116.640118.800276.480
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS108110256
D min/max/mean-3.58611.255-0.000

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Supplemental data

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Sample components

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Entire : Filamentous actin decorated with human cardiac myosin binding pro...

EntireName: Filamentous actin decorated with human cardiac myosin binding protein C C2 domain
Components
  • Complex: Filamentous actin decorated with human cardiac myosin binding protein C C2 domain
    • Complex: Filamentous actin
      • Protein or peptide: Actin, alpha cardiac muscle 1
    • Complex: Cardiac myosin binding protein C C2 domain
      • Protein or peptide: Myosin-binding protein C, cardiac-type

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Supramolecule #1: Filamentous actin decorated with human cardiac myosin binding pro...

SupramoleculeName: Filamentous actin decorated with human cardiac myosin binding protein C C2 domain
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Filamentous actin

SupramoleculeName: Filamentous actin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Sus scrofa (pig)

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Supramolecule #3: Cardiac myosin binding protein C C2 domain

SupramoleculeName: Cardiac myosin binding protein C C2 domain / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human) / Organ: heart

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Macromolecule #1: Actin, alpha cardiac muscle 1

MacromoleculeName: Actin, alpha cardiac muscle 1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 42.064891 KDa
SequenceString: MCDDEETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD G VTHNVPIY ...String:
MCDDEETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD G VTHNVPIY EGYALPHAIM RLDLAGRDLT DYLMKILTER GYSFVTTAER EIVRDIKEKL CYVALDFENE MATAASSSSL EK SYELPDG QVITIGNERF RCPETLFQPS FIGMESAGIH ETTYNSIMKC DIDIRKDLYA NNVLSGGTTM YPGIADRMQK EIT ALAPST MKIKIIAPPE RKYSVWIGGS ILASLSTFQQ MWISKQEYDE AGPSIVHRKC F

UniProtKB: Actin, alpha cardiac muscle 1

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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: 10.499937 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
DEKKSTAFQK KLEPAYQVSK GHKIRLTVEL ADHDAEVKWL KNGQEIQMSG SKYIFESIGA KRTLTISQCS LADDAAYQCV VGGEKCSTE LFVKE

UniProtKB: Myosin-binding protein C, cardiac-type

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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
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 10 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 35.0 e/Å2
Details: Images collected in movie-mode with 44 subframes at 0.85e-2/A per frame
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 27.3 Å
Applied symmetry - Helical parameters - Δ&Phi: -166.5 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: IHRSR / Number images used: 43047
Startup modelType of model: OTHER / Details: randomized azimuthal angles used
Final angle assignmentType: NOT APPLICABLE / Software - Name: SPIDER

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Atomic model buiding 1

Initial model
PDB IDChain

7jh7

source_name: PDB, initial_model_type: experimental model

5k6p

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7lrg:
Filamentous actin decorated with human cardiac myosin binding protein C C2 domain

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