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- PDB-8syf: Homology model of Acto-HMM complex in ADP-state. Chicken smooth m... -

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Basic information

Entry
Database: PDB / ID: 8syf
TitleHomology model of Acto-HMM complex in ADP-state. Chicken smooth muscle HMM and chicken pectoralis actin
Components
  • Actin, alpha skeletal muscle
  • Myosin light polypeptide 6
  • Myosin regulatory light chain 2, smooth muscle major isoform
  • Myosin, heavy chain 11, smooth muscle
KeywordsMOTOR PROTEIN / Actin / Myosin / Smooth muscle / Cryo-EM / Cryo-ET / Heavy meromyosin
Function / homology
Function and homology information


RHO GTPases activate PAKs / myosin II filament / Smooth Muscle Contraction / myofibril assembly / myosin II binding / Striated Muscle Contraction / muscle myosin complex / actomyosin / actomyosin structure organization / myosin complex ...RHO GTPases activate PAKs / myosin II filament / Smooth Muscle Contraction / myofibril assembly / myosin II binding / Striated Muscle Contraction / muscle myosin complex / actomyosin / actomyosin structure organization / myosin complex / myosin II complex / structural constituent of muscle / myosin heavy chain binding / microfilament motor activity / myofibril / cytoskeletal motor activity / striated muscle thin filament / skeletal muscle thin filament assembly / skeletal muscle fiber development / stress fiber / actin filament / ADP binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin filament binding / actin cytoskeleton / hydrolase activity / calcium ion binding / magnesium ion binding / ATP binding / cytoplasm / cytosol
Similarity search - Function
: / 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. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site ...: / 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. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain superfamily / : / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / ATPase, nucleotide binding domain / 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-11 / Myosin light polypeptide 6 / Myosin regulatory light chain 2, smooth muscle major isoform / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 19 Å
AuthorsHojjatian, A. / Taylor, D.W. / Daneshparvar, N. / Trybus, K.M. / Taylor, K.A.
Funding support United States, 9items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)R01 AR47421 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)r01 gm30598 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM139616 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM136288 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10 RR11357 United States
National Science Foundation (NSF, United States)BIR-9512954 United States
National Institutes of Health/Office of the DirectorS10 OD018142 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10 RR025080 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM116788 United States
CitationJournal: J Struct Biol / Year: 2023
Title: Double-headed binding of myosin II to F-actin shows the effect of strain on head structure.
Authors: Alimohammad Hojjatian / Dianne W Taylor / Nadia Daneshparvar / Patricia M Fagnant / Kathleen M Trybus / Kenneth A Taylor /
Abstract: Force production in muscle is achieved through the interaction of myosin and actin. Strong binding states in active muscle are associated with Mg·ADP bound to the active site; release of Mg·ADP ...Force production in muscle is achieved through the interaction of myosin and actin. Strong binding states in active muscle are associated with Mg·ADP bound to the active site; release of Mg·ADP allows rebinding of ATP and dissociation from actin. Thus, Mg·ADP binding is positioned for adaptation as a force sensor. Mechanical loads on the lever arm can affect the ability of myosin to release Mg·ADP but exactly how this is done is poorly defined. Here we use F-actin decorated with double-headed smooth muscle myosin fragments in the presence of Mg·ADP to visualize the effect of internally supplied tension on the paired lever arms using cryoEM. The interaction of the paired heads with two adjacent actin subunits is predicted to place one lever arm under positive and the other under negative strain. The converter domain is believed to be the most flexible domain within myosin head. Our results, instead, point to the segment of heavy chain between the essential and regulatory light chains as the location of the largest structural change. Moreover, our results suggest no large changes in the myosin coiled coil tail as the locus of strain relief when both heads bind F-actin. The method would be adaptable to double-headed members of the myosin family. We anticipate that the study of actin-myosin interaction using double-headed fragments enables visualization of domains that are typically noisy in decoration with single-headed fragments.
History
DepositionMay 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2024Group: Database references / Category: pdbx_related_exp_data_set
Item: _pdbx_related_exp_data_set.data_reference / _pdbx_related_exp_data_set.details
Revision 1.2May 21, 2025Group: Data collection / Structure summary / Category: em_software / pdbx_entry_details / Item: _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myosin, heavy chain 11, smooth muscle
B: Myosin, heavy chain 11, smooth muscle
C: Actin, alpha skeletal muscle
D: Actin, alpha skeletal muscle
E: Myosin light polypeptide 6
F: Myosin regulatory light chain 2, smooth muscle major isoform
G: Myosin regulatory light chain 2, smooth muscle major isoform
H: Myosin light polypeptide 6


Theoretical massNumber of molelcules
Total (without water)343,7088
Polymers343,7088
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Myosin, heavy chain 11, smooth muscle


Mass: 96768.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: MYH11 / Production host: unidentified baculovirus / References: UniProt: A0A8V0ZE13
#2: Protein Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 41862.613 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken)
References: UniProt: P68139, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#3: Protein Myosin light polypeptide 6 / G2 catalytic / LC17-GI / LC17-NM / Myosin light chain alkali smooth-muscle/non-muscle isoforms


Mass: 16639.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: MYL6 / Production host: unidentified baculovirus / References: UniProt: P02607
#4: Protein Myosin regulatory light chain 2, smooth muscle major isoform / MLC-2 / DTNB / G1 / Isoform L20-A


Mass: 16583.412 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: unidentified baculovirus / References: UniProt: P02612
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Filamentous actin decorated with chicken smooth muscle heavy meromyosin
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Gallus gallus (chicken)
Source (recombinant)Organism: unidentified baculovirus
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 200 nm
Image recordingElectron dose: 29.6 e/Å2 / Detector mode: INTEGRATING / Film or detector model: DIRECT ELECTRON DE-64 (8k x 8k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17394 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00923908
ELECTRON MICROSCOPYf_angle_d1.02832244
ELECTRON MICROSCOPYf_dihedral_angle_d6.41214532
ELECTRON MICROSCOPYf_chiral_restr0.0563530
ELECTRON MICROSCOPYf_plane_restr0.0064218

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