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- EMDB-22067: Bovine Cardiac Myosin in Complex with Chicken Skeletal Actin and ... -

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Entry
Database: EMDB / ID: EMD-22067
TitleBovine Cardiac Myosin in Complex with Chicken Skeletal Actin and Human Cardiac Tropomyosin in the Rigor State
Map dataCryo-EM map of the cardiac actin-myosin-tropomyosin complex.
Sample
  • Complex: Helical complex of bovine S1 cardiac myosin and human cardiac tropomyosin-decorated chicken skeletal actin filaments
    • Complex: S1 cardiac myosin
      • Protein or peptide: Tropomyosin alpha-1 chain
    • Complex: cardiac tropomyosin
      • Protein or peptide: Myosin-7
    • Organelle or cellular component: skeletal actin filaments
      • Protein or peptide: Actin, alpha skeletal muscle
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordsmyosin / tropomyosin / actin / cardiac / CONTRACTILE PROTEIN
Function / homology
Function and homology information


positive regulation of heart rate by epinephrine / muscle thin filament tropomyosin / bleb / Striated Muscle Contraction / negative regulation of vascular associated smooth muscle cell migration / regulation of muscle contraction / muscle filament sliding / myosin filament / ruffle organization / myosin II complex ...positive regulation of heart rate by epinephrine / muscle thin filament tropomyosin / bleb / Striated Muscle Contraction / negative regulation of vascular associated smooth muscle cell migration / regulation of muscle contraction / muscle filament sliding / myosin filament / ruffle organization / myosin II complex / adult heart development / Striated Muscle Contraction / positive regulation of ATP-dependent activity / regulation of heart contraction / structural constituent of muscle / sarcomere organization / microfilament motor activity / ventricular cardiac muscle tissue morphogenesis / myofibril / negative regulation of vascular associated smooth muscle cell proliferation / skeletal muscle thin filament assembly / striated muscle thin filament / positive regulation of cell adhesion / Smooth Muscle Contraction / skeletal muscle fiber development / stress fiber / cytoskeleton organization / cardiac muscle contraction / positive regulation of stress fiber assembly / cytoskeletal protein binding / sarcomere / negative regulation of cell migration / actin filament organization / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / wound healing / structural constituent of cytoskeleton / ruffle membrane / cellular response to reactive oxygen species / actin filament binding / actin cytoskeleton / actin binding / regulation of cell shape / cytoskeleton / calmodulin binding / hydrolase activity / protein heterodimerization activity / protein homodimerization activity / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Tropomyosins signature. / Tropomyosin / Tropomyosin / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. ...Tropomyosins signature. / Tropomyosin / Tropomyosin / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / Actins signature 1. / Actin, conserved site / Actins signature 2. / Kinesin motor domain superfamily / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Tropomyosin alpha-1 chain / Actin, alpha skeletal muscle / Myosin-7
Similarity search - Component
Biological speciesBos taurus (cattle) / Homo sapiens (human) / Gallus gallus (chicken)
Methodhelical reconstruction / cryo EM / Resolution: 4.24 Å
AuthorsDoran MH / Lehman W / Bullitt E
Funding support United States, European Union, 7 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL036153 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL123774 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10RR25434 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM129541 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM029090 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM116787 United States
Horizon 2020 Research and Innovation Programme777204 SILICOFCMEuropean Union
CitationJournal: Biophys J / Year: 2020
Title: Cryo-EM and Molecular Docking Shows Myosin Loop 4 Contacts Actin and Tropomyosin on Thin Filaments.
Authors: Matthew H Doran / Elumalai Pavadai / Michael J Rynkiewicz / Jonathan Walklate / Esther Bullitt / Jeffrey R Moore / Michael Regnier / Michael A Geeves / William Lehman /
Abstract: The motor protein myosin drives muscle and nonmuscle motility by binding to and moving along actin of thin filaments. Myosin binding to actin also modulates interactions of the regulatory protein, ...The motor protein myosin drives muscle and nonmuscle motility by binding to and moving along actin of thin filaments. Myosin binding to actin also modulates interactions of the regulatory protein, tropomyosin, on thin filaments, and conversely tropomyosin affects myosin binding to actin. Insight into this reciprocity will facilitate a molecular level elucidation of tropomyosin regulation of myosin interaction with actin in muscle contraction, and in turn, promote better understanding of nonmuscle cell motility. Indeed, experimental approaches such as fiber diffraction, cryoelectron microscopy, and three-dimensional reconstruction have long been used to define regulatory interaction of tropomyosin and myosin on actin at a structural level. However, their limited resolution has not proven sufficient to determine tropomyosin and myosin contacts at an atomic-level and thus to fully substantiate possible functional contributions. To overcome this deficiency, we have followed a hybrid approach by performing new cryogenic electron microscopy reconstruction of myosin-S1-decorated F-actin-tropomyosin together with atomic scale protein-protein docking of tropomyosin to the EM models. Here, cryo-EM data were derived from filaments reconstituted with α1-actin, cardiac αα-tropomyosin, and masseter muscle β-myosin complexes; masseter myosin, which shares sequence identity with β-cardiac myosin-heavy chain, was used because of its stability in vitro. The data were used to build an atomic model of the tropomyosin cable that fits onto the actin filament between the tip of the myosin head and a cleft on the innermost edge of actin subunits. The docking and atomic scale fitting showed multiple discrete interactions of myosin loop 4 and acidic residues on successive 39-42 residue-long tropomyosin pseudorepeats. The contacts between S1 and tropomyosin on actin appear to compete with and displace ones normally found between actin and tropomyosin on myosin-free thin filaments in relaxed muscle, thus restructuring the filament during myosin-induced activation.
History
DepositionMay 27, 2020-
Header (metadata) releaseJul 22, 2020-
Map releaseJul 22, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.01
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  • Surface view with fitted model
  • Atomic models: PDB-6x5z
  • Surface level: 0.01
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6x5z
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22067.png

Downloads & links

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Map

FileDownload / File: emd_22067.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of the cardiac actin-myosin-tropomyosin complex.
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.007 / Movie #1: 0.01
Minimum - Maximum-0.03484657 - 0.058786064
Average (Standard dev.)0.00039920956 (±0.0025944682)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.36 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z271.360271.360271.360
α/β/γ90.00090.00090.000
start NX/NY/NZ434333
NX/NY/NZ116118137
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0350.0590.000

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Supplemental data

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Sample components

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Entire : Helical complex of bovine S1 cardiac myosin and human cardiac tro...

EntireName: Helical complex of bovine S1 cardiac myosin and human cardiac tropomyosin-decorated chicken skeletal actin filaments
Components
  • Complex: Helical complex of bovine S1 cardiac myosin and human cardiac tropomyosin-decorated chicken skeletal actin filaments
    • Complex: S1 cardiac myosin
      • Protein or peptide: Tropomyosin alpha-1 chain
    • Complex: cardiac tropomyosin
      • Protein or peptide: Myosin-7
    • Organelle or cellular component: skeletal actin filaments
      • Protein or peptide: Actin, alpha skeletal muscle
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Helical complex of bovine S1 cardiac myosin and human cardiac tro...

SupramoleculeName: Helical complex of bovine S1 cardiac myosin and human cardiac tropomyosin-decorated chicken skeletal actin filaments
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Bovine myosin was isolated from the masseter muscle and the S1 fragment was generated through proteolytic cleavage.
Molecular weightTheoretical: 403.22 KDa

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Supramolecule #3: S1 cardiac myosin

SupramoleculeName: S1 cardiac myosin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Bos taurus (cattle) / Tissue: Masseter Muscle

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Supramolecule #4: cardiac tropomyosin

SupramoleculeName: cardiac tropomyosin / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: skeletal actin filaments

SupramoleculeName: skeletal actin filaments / type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Gallus gallus (chicken) / Tissue: Breast Skeletal Muscle

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Macromolecule #1: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1
Details: Residues 1-9 and 377 were disordered and were not modeled.
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Gallus gallus (chicken) / Tissue: Breast Skeletal Muscle
Molecular weightTheoretical: 42.096953 KDa
SequenceString: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD G VTHNVPIY ...String:
MCDEDETTAL 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 NNVMSGGTTM YPGIADRMQK EIT ALAPST MKIKIIAPPE RKYSVWIGGS ILASLSTFQQ MWITKQEYDE AGPSIVHRKC F

UniProtKB: Actin, alpha skeletal muscle

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Macromolecule #2: Tropomyosin alpha-1 chain

MacromoleculeName: Tropomyosin alpha-1 chain / type: protein_or_peptide / ID: 2
Details: Only the central section (residues 45-210) was modeled.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.763621 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDAIKKKMQM LKLDKENALD RAEQAEADKK AAEDRSKQLE DELVSLQKKL KGTEDELDKY SEALKDAQEK LELAEKKATD AEADVASLN RRIQLVEEEL DRAQERLATA LQKLEEAEKA ADESERGMKV IESRAQKDEE KMEIQEIQLK EAKHIAEDAD R KYEEVARK ...String:
MDAIKKKMQM LKLDKENALD RAEQAEADKK AAEDRSKQLE DELVSLQKKL KGTEDELDKY SEALKDAQEK LELAEKKATD AEADVASLN RRIQLVEEEL DRAQERLATA LQKLEEAEKA ADESERGMKV IESRAQKDEE KMEIQEIQLK EAKHIAEDAD R KYEEVARK LVIIESDLER AEERAELSEG KCAELEEELK TVTNNLKSLE AQAEKYSQKE DRYEEEIKVL SDKLKEAETR AE FAERSVT KLEKSIDDLE DELYAQKLKY KAISEELDHA LNDMTSI

UniProtKB: Tropomyosin alpha-1 chain

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Macromolecule #3: Myosin-7

MacromoleculeName: Myosin-7 / type: protein_or_peptide / ID: 3
Details: Residues 1-35, 200-216, 624-641, and 777-850 were disordered and not modeled.
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle) / Tissue: Masseter Muscle
Molecular weightTheoretical: 97.446898 KDa
SequenceString: MVDAEMAAFG EAAPYLRKSE KERLEAQTRP FDLKKDVFVP DDKEEFVKAT ILSREGGKVT AETEHGKTVT VKEDQVLQQN PPKFDKIED MAMLTFLHEP AVLYNLKERY ASWMIYTYSG LFCVTINPYK WLPVYNAEVV AAYRGKKRSE APPHIFSISD N AYQYMLTD ...String:
MVDAEMAAFG EAAPYLRKSE KERLEAQTRP FDLKKDVFVP DDKEEFVKAT ILSREGGKVT AETEHGKTVT VKEDQVLQQN PPKFDKIED MAMLTFLHEP AVLYNLKERY ASWMIYTYSG LFCVTINPYK WLPVYNAEVV AAYRGKKRSE APPHIFSISD N AYQYMLTD RENQSILITG ESGAGKTVNT KRVIQYFAVI AAIGDRSKKE QATGKGTLED QIIQANPALE AFGNAKTVRN DN SSRFGKF IRIHFGATGK LASADIETYL LEKSRVIFQL KAERDYHIFY QILSNKKPEL LDMLLITNNP YDYAFISQGE TTV ASIDDA EELMATDNAF DVLGFTTEEK NSMYKLTGAI MHFGNMKFKL KQREEQAEPD GTEEADKSAY LMGLNSADLL KGLC HPRVK VGNEYVTKGQ NVQQVVYAKG ALAKAVYERM FNWMVTRINA TLETKQPRQY FIGVLDIAGF EIFDFNSFEQ LCINF TNEK LQQFFNHHMF VLEQEEYKKE GIEWEFIDFG MDLQACIDLI EKPMGIMSIL EEECMFPKAT DMTFKAKLFD NHLGKS SNF QKPRNIKGKP EAHFSLIHYA GTVDYNIIGW LQKNKDPLNE TVVDLYKKSS LKMLSSLFAN YAGFDTPIEK GKGKAKK GS SFQTVSALHR ENLNKLMTNL RSTHPHFVRC IIPNETKSPG VIDNPLVMHQ LRCNGVLEGI RICRKGFPNR ILYGDFRQ R YRILNPAAIP EGQFIDSRKG AEKLLGSLDI DHNQYKFGHT KVFFKAGLLG LLEEMRDERL SRIITRIQAQ SRGVLSRME FKKLLERRDS LLIIQWNIRA FMGVKNWPWM KLYFKIKPLL KSAETEKEIA

UniProtKB: Myosin-7

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 3 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

Concentration.525 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
50.0 mMCH3COONaSodium Acetate
3.0 mMMgCl2Magnesium Chloride
1.0 mMDithiothreitol
10.0 nMHEPES
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR / Details: Glow discharged using a PELCO easiGlow station
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK III
Details: Thin filaments were reconstituted by first mixing F-actin and tropomyosin to final concentrations of 10 uM actin and 7 uM tropomyosin. Just before applying 1.5 uL actin-tropomyosin to a ...Details: Thin filaments were reconstituted by first mixing F-actin and tropomyosin to final concentrations of 10 uM actin and 7 uM tropomyosin. Just before applying 1.5 uL actin-tropomyosin to a freshly glow discharged holey-carbon grid, the surfactant octyl B-D-glucopyranoside was added to the protein solution to a concentration of 12 nM. The grid sample was manually blotted for 1 second and a 1.5 uL drop of 7.5 uM myosin-S1 sub-fragment was then applied to the blotted grid sample. The sample was immediately blotted for 4 seconds and plunge-frozen in liquid ethane..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 130000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-35 / Number grids imaged: 1 / Number real images: 2496 / Average exposure time: 7.0 sec. / Average electron dose: 53.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Segment selectionNumber selected: 45040 / Software - Name: RELION (ver. 3.0.7)
Startup modelType of model: OTHER / Details: 200 Angstrom Featureless Cylinder
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.0.7)
Final reconstructionApplied symmetry - Helical parameters - Δz: 27.5 Å
Applied symmetry - Helical parameters - Δ&Phi: -166.4 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.24 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Details: Performed in the Relion post-processing step / Number images used: 32158
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

6kn8

source_name: PDB, initial_model_type: experimental modelThe F-actin structure was taken from the Yamada et al. map (PDB ID: 6KN8), fitted within its corresponding density of the masseter S1-decorated actin-tropomyosin reconstruction. A homology model of the beta-myosin S1 was then built based on the rigor-state crystal structure of squid muscle myosin S1 (PDB ID: 3I5G). These models were fit using molecular dynamics flexible fitting in order to align secondary structure elements using VMD 1.9.3. Next, we used Phenix’s Cryo-EM Real Space Refinement in order to refine the MDFF result. Finally, Coot was used to manually refine side chain orientations to reduce clashes, Ramachandran outliers, and sidechain outliers. The tropomyosin backbone was fit into its respective density using UCSF Chimera’s Fit in Map tool. The side chains of tropomyosin included in this structure are based on our extensive protein-protein docking studies found in the associated publication.

3i5g

source_name: PDB, initial_model_type: experimental model
Detailsversion 1.9.3; initial flexible fitting to align secondary structure using MDFF
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6x5z:
Bovine Cardiac Myosin in Complex with Chicken Skeletal Actin and Human Cardiac Tropomyosin in the Rigor State

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Atomic model buiding 2

Detailsversion 1.18-3861
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 70.88
Output model

PDB-6x5z:
Bovine Cardiac Myosin in Complex with Chicken Skeletal Actin and Human Cardiac Tropomyosin in the Rigor State

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Atomic model buiding 3

Detailsmanual refinement of residues to match backbone and sidechain density and to limit clashes, sidechain outliers, and Ramachandran outliers
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-6x5z:
Bovine Cardiac Myosin in Complex with Chicken Skeletal Actin and Human Cardiac Tropomyosin in the Rigor State

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