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- EMDB-42024: CryoEM structure of the Drosophila melanogaster flight muscle myo... -

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Basic information

Entry
Database: EMDB / ID: EMD-42024
TitleCryoEM structure of the Drosophila melanogaster flight muscle myosin filament
Map data
Sample
  • Complex: Drosophila melanogaster flight muscle thick filament
    • Protein or peptide: Flightin
    • Protein or peptide: Myosin
KeywordsStriated muscle / regulatory protein / myosin / flightin / myofilin / stretchin / STRUCTURAL PROTEIN
Function / homology
Function and homology information


myosin ATPase / oscillatory muscle contraction / adult somatic muscle development / striated muscle myosin thick filament assembly / striated muscle myosin thick filament / structural molecule activity conferring elasticity / skeletal muscle myosin thick filament assembly / myosin complex / A band / structural constituent of muscle ...myosin ATPase / oscillatory muscle contraction / adult somatic muscle development / striated muscle myosin thick filament assembly / striated muscle myosin thick filament / structural molecule activity conferring elasticity / skeletal muscle myosin thick filament assembly / myosin complex / A band / structural constituent of muscle / sarcomere organization / cytoskeletal motor activity / isomerase activity / sarcomere / actin filament binding / ATP binding
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. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. ...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 / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Myosin heavy chain, isoform U / Flightin
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsAbbasi Yeganeh F / Rastegarpouyani H / Li J / Taylor KA
Funding support United States, 2 items
OrganizationGrant numberCountry
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
CitationJournal: Int J Mol Sci / Year: 2023
Title: Structure of the Flight Muscle Myosin Filament at 4.7 Å Resolution Reveals New Details of Non-Myosin Proteins.
Authors: Fatemeh Abbasi Yeganeh / Hosna Rastegarpouyani / Jiawei Li / Kenneth A Taylor /
Abstract: Striated muscle thick filaments are composed of myosin II and several non-myosin proteins which define the filament length and modify its function. Myosin II has a globular N-terminal motor domain ...Striated muscle thick filaments are composed of myosin II and several non-myosin proteins which define the filament length and modify its function. Myosin II has a globular N-terminal motor domain comprising its catalytic and actin-binding activities and a long α-helical, coiled tail that forms the dense filament backbone. Myosin alone polymerizes into filaments of irregular length, but striated muscle thick filaments have defined lengths that, with thin filaments, define the sarcomere structure. The motor domain structure and function are well understood, but the myosin filament backbone is not. Here we report on the structure of the flight muscle thick filaments from at 4.7 Å resolution, which eliminates previous ambiguities in non-myosin densities. The full proximal S2 region is resolved, as are the connecting densities between the Ig domains of stretchin-klp. The proteins, flightin, and myofilin are resolved in sufficient detail to build an atomic model based on an AlphaFold prediction. Our results suggest a method by which flightin and myofilin cooperate to define the structure of the thick filament and explains a key myosin mutation that affects flightin incorporation. is a genetic model organism for which our results can define strategies for functional testing.
History
DepositionSep 18, 2023-
Header (metadata) releaseOct 18, 2023-
Map releaseOct 18, 2023-
UpdateNov 1, 2023-
Current statusNov 1, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42024.png

Downloads & links

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Map

FileDownload / File: emd_42024.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.33 Å
Density
Contour LevelBy AUTHOR: 2.79
Minimum - Maximum-4.383524 - 19.048463999999999
Average (Standard dev.)0.027812926 (±0.63307214)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions768768768
Spacing768768768
CellA=B=C: 1021.44006 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_42024_additional_1.map
Projections & Slices
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Additional map: #2

Fileemd_42024_additional_2.map
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Half map: #1

Fileemd_42024_half_map_1.map
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Half map: #2

Fileemd_42024_half_map_2.map
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Sample components

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Entire : Drosophila melanogaster flight muscle thick filament

EntireName: Drosophila melanogaster flight muscle thick filament
Components
  • Complex: Drosophila melanogaster flight muscle thick filament
    • Protein or peptide: Flightin
    • Protein or peptide: Myosin

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Supramolecule #1: Drosophila melanogaster flight muscle thick filament

SupramoleculeName: Drosophila melanogaster flight muscle thick filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Macromolecule #1: Flightin

MacromoleculeName: Flightin / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
SequenceString:
MADEEDPWGF DDGGEEEKAA STQAGTPAPP SKAPSVASDH KADSVVAGTP ANEEAAPEEV EEIKAPPPP PEDDGYRKPV QLYRHWVRPK FLQYKYMYNY RTNYYDDVID YIDKKQTGVA R EIPRPQTW AERVLRTRNI SGSDIDSYAP AKRDKQLIQT LAASIRTYNY HTKAYINQRY AS VL

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Macromolecule #2: Myosin

MacromoleculeName: Myosin / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
SequenceString: MPKPVANQED EDPTPYLFVS LEQRRIDQSK PYDSKKSCWI PDEKEGYLLG EIKATKGDIV SVGLQGGEV RDIKSEKVEK VNPPKFEKIE DMADMTVLNT PCVLHNLRQR YYAKLIYTYS G LFCVAINP YKRYPVYTNR CAKMYRGKRR NEVPPHIFAI SDGAYVDMLT ...String:
MPKPVANQED EDPTPYLFVS LEQRRIDQSK PYDSKKSCWI PDEKEGYLLG EIKATKGDIV SVGLQGGEV RDIKSEKVEK VNPPKFEKIE DMADMTVLNT PCVLHNLRQR YYAKLIYTYS G LFCVAINP YKRYPVYTNR CAKMYRGKRR NEVPPHIFAI SDGAYVDMLT NHVNQSMLIT GE SGAGKTE NTKKVIAYFA TVGASKKTDE AAKSKGSLED QVVQTNPVLE AFGNAKTVRN DNS SRFGKF IRIHFGPTGK LAGADIETYL LEKARVISQQ SLERSYHIFY QIMSGSVPGV KDIC LLTDN IYDYHIVSQG KVTVASIDDA EEFSLTDQAF DILGFTKQEK EDVYRITAAV MHMGG MKFK QRGREEQAEQ DGEEEGGRVS KLFGCDTAEL YKNLLKPRIK VGNEFVTQGR NVQQVT NSI GALCKGVFDR LFKWLVKKCN ETLDTQQKRQ HFIGVLDIAG FEIFEYNGFE QLCINFT NE KLQQFFNHIM FVMEQEEYKK EGINWDFIDF GMDLLACIDL IEKPMGILSI LEEESMFP K ATDQTFSEKL TNTHLGKSAP FQKPKPPKPG QQAAHFAIAH YAGCVSYNIT GWLEKNKDP LNDTVVDQFK KSQNKLLIEI FADHAGQSGG GEQAKGGRGK KGGGFATVSS AYKEQLNSLM TTLRSTQPH FVRCIIPNEM KQPGVVDAHL VMHQLTCNGV LEGIRICRKG FPNRMMYPDF K MRYQILNP RGIKDLDCPK KASKVLIEST ELNEDLYRLG HTKVFFRAGV LGQMEEFRDE RL GKIMSWM QAWARGYLSR KGFKKLQEQR VALKVVQRNL RKYLQLRTWP WYKLWQKVKP LLN VSRIED EIARLEEKAK KAEELHAAEV KVRKELEALN AKLLAEKTAL LDSLSGEKGA LQDY QERNA KLTAQKNDLE NQLRDIQERL TQEEDARNQL FQQKKKADQE ISGLKKDIED LELNV QKAE QDKATKDHQI RNLNDEIAHQ DELINKLNKE KKMQGETNQK TGEELQAAED KINHLN KVK AKLEQTLDEL EDSLEREKKV RGDVEKSKRK VEGDLKLTQE AVADLERNKK ELEQTIQ RK DKELSSITAK LEDEQVVVLK HQRQIKELQA RIEELEEEVE AERQARAKAE KQRADLAR E LEELGERLEE AGGATSAQIE LNKKREAELS KLRRDLEEAN IQHESTLANL RKKHNDAVA EMAEQVDQLN KLKAKAEHDR QTCHNELNQT RTACDQLGRD KAAQEKIAKQ LQHTLNEVQS KLDETNRTL NDFDASKKKL SIENSDLLRQ LEEAESQVSQ LSKIKISLTT QLEDTKRLAD E ESRERATL LGKFRNLEHD LDNLREQVEE EAEGKADLQR QLSKANAEAQ VWRSKYESDG VA RSEELEE AKRKLQARLA EAEETIESLN QKCIGLEKTK QRLSTEVEDL QLEVDRANAI ANA AEKKQK AFDKIIGEWK LKVDDLAAEL DASQKECRNY STELFRLKGA YEEGQEQLEA VRRE NKNLA DEVKDLLDQI GEGGRNIHEI EKARKRLEAE KDELQAALEE AEAALEQEEN KVLRA QLEL SQVRQEIDRR IQEKEEEFEN TRKNHQRALD SMQASLEAEA KGKAEALRMK KKLEAD INE LEIALDHANK ANAEAQKNIK RYQQQLKDIQ TALEEEQRAR DDAREQLGIS ERRANAL QN ELEESRTLLE QADRGRRQAE QELADAHEQL NEVSAQNASI SAAKRKLESE LQTLHSDL D ELLNEAKNSE EKAKKAMVDA ARLADELRAE QDHAQTQEKL RKALEQQIKE LQVRLDEAE ANALKGGKKA IQKLEQRVRE LENELDGEQR RHADAQKNLR KSERRVKELS FQSEEDRKNH ERMQDLVDK LQQKIKTYKR QIEEAEEIAA LNLAKFRKAQ QELEEAEERA DLAEQAISKF R AKGRAGSV GRGASPAPRA TSVRPQFDGL AFPPRFDLAP ENEF

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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 R2/1 / Material: COPPER
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 138000
Startup modelType of model: OTHER / Details: ab-initio model
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: OTHER / Number images used: 116000

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8u8h:
The structure of flightin within myosin thick filaments from Drosophila melanogaster flight muscle

PDB-8u95:
The structure of myosin heavy chain from Drosophila melanogaster flight muscle thick filaments

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