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- PDB-7kog: Lethocerus Myosin II complete coiled-coil domain resolved in its ... -

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Entry
Database: PDB / ID: 7kog
TitleLethocerus Myosin II complete coiled-coil domain resolved in its native environment
ComponentsMyosin heavy chain isoform Mhc_X1
KeywordsMOTOR PROTEIN / striated muscle / asynchronous flight muscle
Biological speciesLethocerus indicus (insect)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.25 Å
AuthorsRahmani, H. / Hu, Z. / Daneshparvar, N. / Taylor, D. / Taylor, K.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM30598 United States
American Heart Association20PRE35120273 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: The myosin II coiled-coil domain atomic structure in its native environment.
Authors: Hamidreza Rahmani / Wen Ma / Zhongjun Hu / Nadia Daneshparvar / Dianne W Taylor / J Andrew McCammon / Thomas C Irving / Robert J Edwards / Kenneth A Taylor /
Abstract: The atomic structure of the complete myosin tail within thick filaments isolated from flight muscle is described and compared to crystal structures of recombinant, human cardiac myosin tail segments. ...The atomic structure of the complete myosin tail within thick filaments isolated from flight muscle is described and compared to crystal structures of recombinant, human cardiac myosin tail segments. Overall, the agreement is good with three exceptions: the proximal S2, in which the filament has heads attached but the crystal structure doesn't, and skip regions 2 and 4. At the head-tail junction, the tail α-helices are asymmetrically structured encompassing well-defined unfolding of 12 residues for one myosin tail, ∼4 residues of the other, and different degrees of α-helix unwinding for both tail α-helices, thereby providing an atomic resolution description of coiled-coil "uncoiling" at the head-tail junction. Asymmetry is observed in the nonhelical C termini; one C-terminal segment is intercalated between ribbons of myosin tails, the other apparently terminating at Skip 4 of another myosin tail. Between skip residues, crystal and filament structures agree well. Skips 1 and 3 also agree well and show the expected α-helix unwinding and coiled-coil untwisting in response to skip residue insertion. Skips 2 and 4 are different. Skip 2 is accommodated in an unusual manner through an increase in α-helix radius and corresponding reduction in rise/residue. Skip 4 remains helical in one chain, with the other chain unfolded, apparently influenced by the acidic myosin C terminus. The atomic model may shed some light on thick filament mechanosensing and is a step in understanding the complex roles that thick filaments of all species undergo during muscle contraction.
History
DepositionNov 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
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Revision 1.1Mar 31, 2021Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.2Apr 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3May 29, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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Assembly

Deposited unit
B: Myosin heavy chain isoform Mhc_X1
A: Myosin heavy chain isoform Mhc_X1


Theoretical massNumber of molelcules
Total (without water)450,4552
Polymers450,4552
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: No experiment was needed since the helical symmetry was observed in the cryoEM structure without prior assumption.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area47240 Å2
ΔGint-486 kcal/mol
Surface area158200 Å2

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Components

#1: Protein Myosin heavy chain isoform Mhc_X1


Mass: 225227.562 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lethocerus indicus (insect)
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: Lethocerus flight muscle myosin filament / Type: ORGANELLE OR CELLULAR COMPONENT
Details: The sample is a bipolar helical structure, with helical repeat 145 Angstrom and helical turn 33.98 degree. The sample has C4 symmetry. The map contains 6 unique features: myosin molecule ...Details: The sample is a bipolar helical structure, with helical repeat 145 Angstrom and helical turn 33.98 degree. The sample has C4 symmetry. The map contains 6 unique features: myosin molecule with completely resolved rods, 4 resolved non-myosin densities among the myosin rods and an annular region inside of annulus occupied by myosin rods that most likely contains paramyosin. The 4 non-myosin densities may contain parts of the proteins myofilin and flightin.
Entity ID: all / Source: NATURAL
Molecular weightUnits: KILODALTONS/NANOMETER / Experimental value: NO
Source (natural)Organism: Lethocerus indicus (insect) / Cellular location: myofibril / Organ: myocyte / Organelle: Sarcomere / Tissue: dorsal longitudinal indirect flight muscle
Buffer solutionpH: 6.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 FIELD
Image recordingElectron dose: 60 e/Å2 / Detector mode: INTEGRATING / Film or detector model: DIRECT ELECTRON DE-64 (8k x 8k) / Num. of grids imaged: 1 / Num. of real images: 3507
Image scansWidth: 8192 / Height: 8192 / Movie frames/image: 34 / Used frames/image: 1-34

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
EM software
IDNameCategory
4GctfCTF correction
8PHENIXmodel refinement
13cisTEM3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 173515 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00517496
ELECTRON MICROSCOPYf_angle_d0.65323341
ELECTRON MICROSCOPYf_dihedral_angle_d13.6792324
ELECTRON MICROSCOPYf_chiral_restr0.0372591
ELECTRON MICROSCOPYf_plane_restr0.0033166

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