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- PDB-8ew5: The structure of flightin within myosin thick filaments from Bomb... -

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Basic information

Entry
Database: PDB / ID: 8ew5
TitleThe structure of flightin within myosin thick filaments from Bombus ignitus flight muscle
ComponentsFlightin
KeywordsSTRUCTURAL PROTEIN / Striated muscle / regulatory protein / myosin-binding protein
Biological speciesBombus ignitus (insect)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6 Å
AuthorsLi, J. / Rahmani, H. / Abbasi Yeganeh, F. / Rastegarpouyani, H. / Taylor, D.W. / Wood, N.B. / Previs, M.J. / Iwamoto, H. / Taylor, K.A.
Funding support Japan, United States, 7items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19K06777 Japan
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM030598 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 Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)R21 AR077802 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01 HL157487 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM116788 United States
American Heart Association20PRE35120273 United States
CitationJournal: Int J Mol Sci / Year: 2022
Title: Structure of the Flight Muscle Thick Filament from the Bumble Bee, , at 6 Å Resolution.
Authors: Jiawei Li / Hamidreza Rahmani / Fatemeh Abbasi Yeganeh / Hosna Rastegarpouyani / Dianne W Taylor / Neil B Wood / Michael J Previs / Hiroyuki Iwamoto / Kenneth A Taylor /
Abstract: Four insect orders have flight muscles that are both asynchronous and indirect; they are asynchronous in that the wingbeat frequency is decoupled from the frequency of nervous stimulation and ...Four insect orders have flight muscles that are both asynchronous and indirect; they are asynchronous in that the wingbeat frequency is decoupled from the frequency of nervous stimulation and indirect in that the muscles attach to the thoracic exoskeleton instead of directly to the wing. Flight muscle thick filaments from two orders, Hemiptera and Diptera, have been imaged at a subnanometer resolution, both of which revealed a myosin tail arrangement referred to as “curved molecular crystalline layers”. Here, we report a thick filament structure from the indirect flight muscles of a third insect order, Hymenoptera, the Asian bumble bee Bombus ignitus. The myosin tails are in general agreement with previous determinations from Lethocerus indicus and Drosophila melanogaster. The Skip 2 region has the same unusual structure as found in Lethocerus indicus thick filaments, an α-helix discontinuity is also seen at Skip 4, but the orientation of the Skip 1 region on the surface of the backbone is less angled with respect to the filament axis than in the other two species. The heads are disordered as in Drosophila, but we observe no non-myosin proteins on the backbone surface that might prohibit the ordering of myosin heads onto the thick filament backbone. There are strong structural similarities among the three species in their non-myosin proteins within the backbone that suggest how one previously unassigned density in Lethocerus might be assigned. Overall, the structure conforms to the previously observed pattern of high similarity in the myosin tail arrangement, but differences in the non-myosin proteins.
History
DepositionOct 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3May 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

Downloads & links

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Assembly

Deposited unit
A: Flightin


Theoretical massNumber of molelcules
Total (without water)18,3971
Polymers18,3971
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, The model is built on the segment density of flightin from the Bombus ignitus thick filament map.
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Flightin


Mass: 18396.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bombus ignitus (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: Bombus ignitus flight muscle thick filament / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Bombus ignitus (insect)
Buffer solutionpH: 6.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil
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 / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20_4459: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 11000
3D reconstructionResolution: 6 Å / Resolution method: OTHER / Num. of particles: 11000 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0041035
ELECTRON MICROSCOPYf_angle_d0.8211397
ELECTRON MICROSCOPYf_dihedral_angle_d6.224138
ELECTRON MICROSCOPYf_chiral_restr0.049129
ELECTRON MICROSCOPYf_plane_restr0.009178

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