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- EMDB-28208: CryoEM map of myosin thick filament from Bombus ignitus asynchron... -

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Basic information

Entry
Database: EMDB / ID: EMD-28208
TitleCryoEM map of myosin thick filament from Bombus ignitus asynchronous flight muscle
Map dataIt is the sharpened map of Bombus thick filament with helical imposing. It is the final map we used for segmentation and analysis.
Sample
  • Complex: Bombus ignitus flight muscle thick filament
Keywordscoiled coil / striated muscle / ATPase / actin-binding protein / CONTRACTILE PROTEIN
Biological speciesBombus ignitus (insect)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.0 Å
AuthorsLi J / Rahmani H / Abbasi Yeganeh F / Rastegarpouyani H / Taylor DW / Wood NB / Previs MJ / Iwamoto H / Taylor KA
Funding support Japan, United States, 7 items
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
DepositionSep 21, 2022-
Header (metadata) releaseJan 4, 2023-
Map releaseJan 4, 2023-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28208.png

Downloads & links

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Map

FileDownload / File: emd_28208.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIt is the sharpened map of Bombus thick filament with helical imposing. It is the final map we used for segmentation and analysis.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 768 pix.
= 829.44 Å		1.08 Å/pix.
x 768 pix.
= 829.44 Å		1.08 Å/pix.
x 768 pix.
= 829.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-0.7690356 - 19.365390000000001
Average (Standard dev.)0.026866268 (±0.50294507)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions768768768
Spacing768768768
CellA=B=C: 829.44006 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: This is a segment map of non-myosin protein...

Fileemd_28208_additional_1.map
AnnotationThis is a segment map of non-myosin protein - flightin, from the primary Bombus thick filament map, the corresponding model will be deposited in another entry.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: It is the first half map of Bombus...

Fileemd_28208_half_map_1.map
AnnotationIt is the first half map of Bombus thick filament without any post-processing.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: It is the second half map of Bombus...

Fileemd_28208_half_map_2.map
AnnotationIt is the second half map of Bombus thick filament without any post-processing.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Bombus ignitus flight muscle thick filament

EntireName: Bombus ignitus flight muscle thick filament
Components
  • Complex: Bombus ignitus flight muscle thick filament

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Supramolecule #1: Bombus ignitus flight muscle thick filament

SupramoleculeName: Bombus ignitus flight muscle thick filament / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Bombus ignitus (insect)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 6.8
GridModel: Quantifoil / Material: COPPER
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 11000
Startup modelType of model: OTHER
Details: low-pass filtered Lethocerus myosin thick filament map
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: OTHER / Number images used: 11000
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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