[English] 日本語
Yorodumi
- EMDB-47369: The structure of myosin thick filament from Drosophila melanogast... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-47369
TitleThe structure of myosin thick filament from Drosophila melanogaster flight muscle with disordered arrangement of myosin heads
Map dataDrosophila flight muscle thick filament with disordered arrangement of myosin heads. This is the final map we used for segmentation and analysis.
Sample
  • Complex: Drosophila melanogaster flight muscle thick filament
    • Protein or peptide: Myosin heavy chain, isoform U
Keywordsaging / flightin / myofilin / paramyosin / stretchin-klp / STRUCTURAL PROTEIN
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsRastegarpouyani H / Hojjatian A / Taylor KA
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM139616 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM116788 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R24 GM154192 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM129539 United States
Simons FoundationSF349247 United States
CitationJournal: Int J Mol Sci / Year: 2024
Title: Two Forms of Thick Filament in the Flight Muscle of .
Authors: Hosna Rastegarpouyani / Alimohammad Hojjatian / Kenneth A Taylor /
Abstract: Invertebrate striated muscle myosin filaments are highly variable in structure. The best characterized myosin filaments are those found in insect indirect flight muscle (IFM) in which the flight- ...Invertebrate striated muscle myosin filaments are highly variable in structure. The best characterized myosin filaments are those found in insect indirect flight muscle (IFM) in which the flight-powering muscles are not attached directly to the wings. Four insect orders, Hemiptera, Diptera, Hymenoptera, and Coleoptera, have evolved IFM. IFM thick filaments from the first three orders have highly similar myosin arrangements but differ significantly among their non-myosin proteins. The cryo-electron microscopy of isolated IFM myosin filaments from the Dipteran described here revealed the coexistence of two distinct filament types, one presenting a tubular backbone like in previous work and the other a solid backbone. Inside an annulus of myosin tails, tubular filaments show no noticeable densities; solid filaments show four paired paramyosin densities. Both myosin heads of the tubular filaments are disordered; solid filaments have one completely and one partially immobilized head. Tubular filaments have the protein stretchin-klp on their surface; solid filaments do not. Two proteins, flightin and myofilin, are identifiable in all the IFM filaments previously determined. In , flightin assumes two conformations, being compact in solid filaments and extended in tubular filaments. Nearly identical solid filaments occur in the large water bug , which flies infrequently. The tubular filaments occur in younger flies, and the solid filaments appear in older flies, which fly less frequently if at all, suggesting that the solid filament form is correlated with infrequent muscle use. We suggest that the solid form is designed to conserve ATP when the muscle is not in active use.
History
DepositionOct 19, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_47369.png

Downloads & links

-
Map

FileDownload / File: emd_47369.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDrosophila flight muscle thick filament with disordered arrangement of myosin heads. This is the final map we used for segmentation and analysis.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 768 pix.
= 736.512 Å		0.96 Å/pix.
x 768 pix.
= 736.512 Å		0.96 Å/pix.
x 768 pix.
= 736.512 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.959 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.11097546 - 3.15743
Average (Standard dev.)0.0025413139 (±0.06498383)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions768768768
Spacing768768768
CellA=B=C: 736.51196 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: It is the first half map of Drosophila...

Fileemd_47369_half_map_1.map
AnnotationIt is the first half map of Drosophila flight muscle thick filament with disordered arrangement of myosin heads without any post-processing.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: It is the second half map of Drosophila...

Fileemd_47369_half_map_2.map
AnnotationIt is the second half map of Drosophila flight muscle thick filament with disordered arrangement of myosin heads without any post-processing.
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: Myosin heavy chain, isoform U

-
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: Myosin heavy chain, isoform U

MacromoleculeName: Myosin heavy chain, isoform U / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
SequenceString: MPKPVANQED EDPTPYLFVS LEQRRIDQSK PYDSKKSCWI PDEKEGYLLG EIKATKGDIV SVGLQGGETR DLKKDLLQQV NPPKYEKAE DMSNLTYLND ASVLHNLRQR YYNKLIYTYS GLFCVAINPY KRYPVYTNRC AKMYRGKRRN EVPPHIFAIS D GAYVDMLT ...String:
MPKPVANQED EDPTPYLFVS LEQRRIDQSK PYDSKKSCWI PDEKEGYLLG EIKATKGDIV SVGLQGGETR DLKKDLLQQV NPPKYEKAE DMSNLTYLND ASVLHNLRQR YYNKLIYTYS GLFCVAINPY KRYPVYTNRC AKMYRGKRRN EVPPHIFAIS D GAYVDMLT NHVNQSMLIT GESGAGKTEN TKKVIAYFAT VGASKKTDEA AKSKGSLEDQ VVQTNPVLEA FGNAKTVRND NS SRFGKFI RIHFGPTGKL AGADIETYLL EKARVISQQS LERSYHIFYQ IMSGSVPGVK DICLLTDNIY DYHIVSQGKV TVA SIDDAE EFSLTDQAFD ILGFTKQEKE DVYRITAAVM HMGGMKFKQR GREEQAEQDG EEEGGRVSKL FGCDTAELYK NLLK PRIKV GNEFVTQGRN VQQVTNSIGA LCKGVFDRLF KWLVKKCNET LDTQQKRQHF IGVLDIAGFE IFEYNGFEQL CINFT NEKL QQFFNHHMFV LEQEEYKREG IDWAFIDFGM DLLACIDLIE KPMGILSILE EESMFPKATD QTFSEKLTNT HLGKSA PFQ KPKPPKPGQQ AAHFAIAHYA GCVSYNITGW LEKNKDPLND TVVDQFKKSQ NKLLIEIFAD HAGQSGGGEQ AKGGRGK KG GGFATVSSAY KEQLNSLMTT LRSTQPHFVR CIIPNEMKQP GVVDAHLVMH QLTCNGVLEG IRICRKGFPN RMMYPDFK M RYQILNPKGI KGIEDPKKCT KVLIESTELN DDQYRLGNTK VFFRAGVLGQ MEEFRDERLG KIMSWMQAWA RGYLSRKGF KKLQEQRVAL KVVQRNLRKY LQLRTWPWYK LWQKVKPLLN VSRIEDEIAR LEEKAKKAEE LHAAEVKVRK ELEALNAKLL AEKTALLDS LSGEKGALQD YQERNAKLTA QKNDLENQLR DIQERLTQEE DARNQLFQQK KKADQEISGL KKDIEDLELN V QKAEQDKA TKDHQIRNLN DEIAHQDELI NKLNKEKKMQ GETNQKTGEE LQAAEDKINH LNKVKAKLEQ TLDELEDSLE RE KKVRGDV EKSKRKVEGD LKLTQEAVAD LERNKKELEQ TIQRKDKELS SITAKLEDEQ VVVLKHQRQI KELQARIEEL EEE VEAERQ ARAKAEKQRA DLARELEELG ERLEEAGGAT SAQIELNKKR EAELSKLRRD LEEANIQHES TLANLRKKHN DAVA EMAEQ VDQLNKLKAK AEKEKNEYYG QLNDLRAGVD HITNEKAAQE KIAKQLQHTL NEVQSKLDET NRTLNDFDAS KKKLS IENS DLLRQLEEAE SQVSQLSKIK ISLTTQLEDT KRLADEESRE RATLLGKFRN LEHDLDNLRE QVEEEAEGKA DLQRQL SKA NAEAQVWRSK YESDGVARSE ELEEAKRKLQ ARLAEAEETI ESLNQKCIGL EKTKQRLSTE VEDLQLEVDR ANAIANA AE KKQKAFDKII GEWKLKVDDL AAELDASQKE CRNYSTELFR LKGAYEEGQE QLEAVRRENK NLADEVKDLL DQIGEGGR N IHEIEKARKR LEAEKDELQA ALEEAEAALE QEENKVLRAQ LELSQVRQEI DRRIQEKEEE FENTRKNHQR ALDSMQASL EAEAKGKAEA LRMKKKLEAD INELEIALDH ANKANAEAQK NIKRYQQQLK DIQTALEEEQ RARDDAREQL GISERRANAL QNELEESRT LLEQADRGRR QAEQELADAH EQLNEVSAQN ASISAAKRKL ESELQTLHSD LDELLNEAKN SEEKAKKAMV D AARLADEL RAEQDHAQTQ EKLRKALEQQ IKELQVRLDE AEANALKGGK KAIQKLEQRV RELENELDGE QRRHADAQKN LR KSERRVK ELSFQSEEDR KNHERMQDLV DKLQQKIKTY KRQIEEAEEI AALNLAKFRK AQQELEEAEE RADLAEQAIS KFR AKGRAG SVGRGASPAP TASKGRKSAL LEQ

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 6.8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 45.0 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

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: OTHER / Number images used: 255577
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING

+
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