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- PDB-7nep: Homology model of the in situ actomyosin complex from the A-band ... -

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Basic information

Entry
Database: PDB / ID: 7nep
TitleHomology model of the in situ actomyosin complex from the A-band of mouse psoas muscle sarcomere in the rigor state
Components
  • Actin, alpha skeletal muscle
  • Myosin light chain 1/3, skeletal muscle isoform
  • Myosin regulatory light chain 2, skeletal muscle isoform
  • Myosin-4
  • Tropomyosin alpha-1 chain
KeywordsMOTOR PROTEIN / Muscle proteins / force generation / sarcomere / cytoskeleton
Function / homology
Function and homology information


positive regulation of heart rate by epinephrine / muscle thin filament tropomyosin / skeletal muscle fiber adaptation / Striated Muscle Contraction / Smooth Muscle Contraction / contractile muscle fiber / bleb / negative regulation of vascular associated smooth muscle cell migration / muscle filament sliding / cellular response to organonitrogen compound ...positive regulation of heart rate by epinephrine / muscle thin filament tropomyosin / skeletal muscle fiber adaptation / Striated Muscle Contraction / Smooth Muscle Contraction / contractile muscle fiber / bleb / negative regulation of vascular associated smooth muscle cell migration / muscle filament sliding / cellular response to organonitrogen compound / myosin filament / response to extracellular stimulus / actin filament capping / ruffle organization / myosin II complex / response to steroid hormone / myosin complex / structural constituent of muscle / sarcomere organization / microfilament motor activity / ventricular cardiac muscle tissue morphogenesis / myofibril / mesenchyme migration / negative regulation of vascular associated smooth muscle cell proliferation / skeletal muscle thin filament assembly / striated muscle thin filament / positive regulation of cell adhesion / skeletal muscle fiber development / response to mechanical stimulus / skeletal muscle tissue development / stress fiber / cardiac muscle contraction / positive regulation of stress fiber assembly / cytoskeletal protein binding / sarcomere / negative regulation of cell migration / response to activity / filopodium / muscle contraction / 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 / disordered domain specific binding / actin filament binding / actin cytoskeleton / double-stranded RNA binding / lamellipodium / cell body / actin binding / regulation of cell shape / in utero embryonic development / calmodulin binding / hydrolase activity / immune response / protein heterodimerization activity / calcium ion binding / positive regulation of gene expression / protein homodimerization activity / protein-containing complex / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Tropomyosins signature. / Tropomyosin / Tropomyosin / EF-hand domain / 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 ...Tropomyosins signature. / Tropomyosin / Tropomyosin / EF-hand domain / 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 / EF-hand, calcium binding motif / ATPase, nucleotide binding domain / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Myosin light chain 1/3, skeletal muscle isoform / Tropomyosin alpha-1 chain / Actin, alpha skeletal muscle / Myosin regulatory light chain 11 / Myosin-4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 10.2 Å
AuthorsWang, Z. / Grange, M. / Wagner, T. / Kho, A.L. / Gautel, M. / Raunser, S.
Funding support Germany, United Kingdom, European Union, 5items
OrganizationGrant numberCountry
Max Planck Society Germany
Wellcome Trust201543/Z/16/Z United Kingdom
European Research Council (ERC)856118European Union
Medical Research Council (MRC, United Kingdom)MR/R003106/1 United Kingdom
European Molecular Biology Organization (EMBO)ALTF 693-2018European Union
CitationJournal: Cell / Year: 2021
Title: The molecular basis for sarcomere organization in vertebrate skeletal muscle.
Authors: Zhexin Wang / Michael Grange / Thorsten Wagner / Ay Lin Kho / Mathias Gautel / Stefan Raunser /
Abstract: Sarcomeres are force-generating and load-bearing devices of muscles. A precise molecular picture of how sarcomeres are built underpins understanding their role in health and disease. Here, we ...Sarcomeres are force-generating and load-bearing devices of muscles. A precise molecular picture of how sarcomeres are built underpins understanding their role in health and disease. Here, we determine the molecular architecture of native vertebrate skeletal sarcomeres by electron cryo-tomography. Our reconstruction reveals molecular details of the three-dimensional organization and interaction of actin and myosin in the A-band, I-band, and Z-disc and demonstrates that α-actinin cross-links antiparallel actin filaments by forming doublets with 6-nm spacing. Structures of myosin, tropomyosin, and actin at ~10 Å further reveal two conformations of the "double-head" myosin, where the flexible orientation of the lever arm and light chains enable myosin not only to interact with the same actin filament, but also to split between two actin filaments. Our results provide unexpected insights into the fundamental organization of vertebrate skeletal muscle and serve as a strong foundation for future investigations of muscle diseases.
History
DepositionFeb 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
B: Actin, alpha skeletal muscle
C: Actin, alpha skeletal muscle
D: Actin, alpha skeletal muscle
E: Actin, alpha skeletal muscle
F: Actin, alpha skeletal muscle
G: Actin, alpha skeletal muscle
H: Actin, alpha skeletal muscle
I: Actin, alpha skeletal muscle
J: Actin, alpha skeletal muscle
K: Actin, alpha skeletal muscle
P: Tropomyosin alpha-1 chain
Q: Tropomyosin alpha-1 chain
T: Tropomyosin alpha-1 chain
U: Tropomyosin alpha-1 chain
L: Myosin-4
N: Myosin light chain 1/3, skeletal muscle isoform
R: Myosin regulatory light chain 2, skeletal muscle isoform
M: Myosin-4
O: Myosin light chain 1/3, skeletal muscle isoform
S: Myosin regulatory light chain 2, skeletal muscle isoform


Theoretical massNumber of molelcules
Total (without water)825,74821
Polymers825,74821
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area71750 Å2
ΔGint-552 kcal/mol
Surface area319070 Å2
MethodPISA

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Components

#1: Protein
Actin, alpha skeletal muscle / / Alpha-actin-1


Mass: 41747.527 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P68134
#2: Protein
Tropomyosin alpha-1 chain / Alpha-tropomyosin / Tropomyosin-1


Mass: 28922.074 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P58771
#3: Protein Myosin-4 / / Myosin heavy chain 2b / MyHC-2b / Myosin heavy chain 4


Mass: 92518.234 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q5SX39
#4: Protein Myosin light chain 1/3, skeletal muscle isoform / MLC1F/MLC3F / Myosin light chain alkali 1/2 / Myosin light chain A1/A2


Mass: 16573.590 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P05977
#5: Protein Myosin regulatory light chain 2, skeletal muscle isoform / Fast skeletal myosin light chain 2 / MLC2F


Mass: 16326.439 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P97457

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: subtomogram averaging

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1In situ actomyosin complex in the rigor state from mouse psoas muscleCOMPLEXall0NATURAL
2actinCOMPLEX#11NATURAL
3myosin double headCOMPLEX#3-#51NATURAL
4tropomyosinCOMPLEX#21NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
41NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Mus musculus (house mouse)10090
32Mus musculus (house mouse)10090
43Mus musculus (house mouse)10090
54Mus musculus (house mouse)10090
Buffer solutionpH: 7
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2140 mMpotassium chlorideKCl1
32 mMmagnesium chlorideMgCl21
41 mMegtazic acidEGTA1
51 mMdithiothreitolDTT1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: The sample was myofibrils.
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 286 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 FIELDBright-field microscopy / Nominal magnification: 81000 X / Calibrated magnification: 28409 X / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 3.5 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansWidth: 3710 / Height: 3838 / Movie frames/image: 8 / Used frames/image: 1-8

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Processing

EM software
IDNameVersionCategory
2SerialEM3.7.5image acquisition
4IMODCTF correction
7UCSF Chimeramodel fitting
10RELION3.0.4final Euler assignment
11RELION3.0.4classification
12RELION3.0.43D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 10.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18090 / Algorithm: BACK PROJECTION / Symmetry type: POINT
EM volume selectionNum. of tomograms: 8 / Num. of volumes extracted: 32421
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model building
IDPDB-ID 3D fitting-ID
15JLH

5jlh

1
26KN8

6kn8

1
33I5G

3i5g

1

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