[English] 日本語
Yorodumi
- EMDB-42024: CryoEM structure of the Drosophila melanogaster flight muscle myo... -

+
Open data


ID or keywords:

Loading...

-
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 / cellular component assembly / anatomical structure formation involved in morphogenesis / striated muscle myosin thick filament / structural molecule activity conferring elasticity / A band / myosin filament ...myosin ATPase / oscillatory muscle contraction / adult somatic muscle development / striated muscle myosin thick filament assembly / cellular component assembly / anatomical structure formation involved in morphogenesis / striated muscle myosin thick filament / structural molecule activity conferring elasticity / A band / myosin filament / myosin complex / structural constituent of muscle / sarcomere organization / cytoskeletal motor activity / isomerase activity / supramolecular fiber organization / sarcomere / actin filament binding / actin cytoskeleton organization / 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. / 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

-
Structure visualization

Supplemental images

emd_42024.png

Downloads & links

-
Map

FileDownload / File: emd_42024.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 768 pix.
= 1021.44 Å		1.33 Å/pix.
x 768 pix.
= 1021.44 Å		1.33 Å/pix.
x 768 pix.
= 1021.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.33 Å
Density

Histogram

Histogram (log scale)
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 °

-
Supplemental data

-
Additional map: #1

Fileemd_42024_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #2

Fileemd_42024_additional_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_42024_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_42024_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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)

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 6.8
GridModel: Quantifoil R2/1 / Material: COPPER
VitrificationCryogen name: ETHANE

-
Electron microscopy

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

+
Image processing

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more