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- EMDB-22975: Lethocerus Myosin II complete coiled-coil domain resolved in its ... -

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Basic information

Entry
Database: EMDB / ID: EMD-22975
TitleLethocerus Myosin II complete coiled-coil domain resolved in its native environment
Map dataOne myosin molecule segmented out of the helically extended reconstruction
Sample
  • Organelle or cellular component: Lethocerus flight muscle myosin filament
    • Protein or peptide: Myosin heavy chain isoform Mhc_X1
Biological speciesLethocerus indicus (insect)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.25 Å
AuthorsRahmani H / Hu Z / Daneshparvar N / Taylor D / Taylor KA
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM30598 United States
American Heart Association20PRE35120273 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: The myosin II coiled-coil domain atomic structure in its native environment.
Authors: Hamidreza Rahmani / Wen Ma / Zhongjun Hu / Nadia Daneshparvar / Dianne W Taylor / J Andrew McCammon / Thomas C Irving / Robert J Edwards / Kenneth A Taylor /
Abstract: The atomic structure of the complete myosin tail within thick filaments isolated from flight muscle is described and compared to crystal structures of recombinant, human cardiac myosin tail segments. ...The atomic structure of the complete myosin tail within thick filaments isolated from flight muscle is described and compared to crystal structures of recombinant, human cardiac myosin tail segments. Overall, the agreement is good with three exceptions: the proximal S2, in which the filament has heads attached but the crystal structure doesn't, and skip regions 2 and 4. At the head-tail junction, the tail α-helices are asymmetrically structured encompassing well-defined unfolding of 12 residues for one myosin tail, ∼4 residues of the other, and different degrees of α-helix unwinding for both tail α-helices, thereby providing an atomic resolution description of coiled-coil "uncoiling" at the head-tail junction. Asymmetry is observed in the nonhelical C termini; one C-terminal segment is intercalated between ribbons of myosin tails, the other apparently terminating at Skip 4 of another myosin tail. Between skip residues, crystal and filament structures agree well. Skips 1 and 3 also agree well and show the expected α-helix unwinding and coiled-coil untwisting in response to skip residue insertion. Skips 2 and 4 are different. Skip 2 is accommodated in an unusual manner through an increase in α-helix radius and corresponding reduction in rise/residue. Skip 4 remains helical in one chain, with the other chain unfolded, apparently influenced by the acidic myosin C terminus. The atomic model may shed some light on thick filament mechanosensing and is a step in understanding the complex roles that thick filaments of all species undergo during muscle contraction.
History
DepositionNov 9, 2020-
Header (metadata) releaseMar 24, 2021-
Map releaseMar 24, 2021-
UpdateApr 14, 2021-
Current statusApr 14, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7kog
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7kog
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22975.png

Downloads & links

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Map

FileDownload / File: emd_22975.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOne myosin molecule segmented out of the helically extended reconstruction
Voxel sizeX=Y=Z: 0.98 Å
Density
Contour LevelBy AUTHOR: 0.12 / Movie #1: 0.12
Minimum - Maximum-0.07149465 - 3.2776268
Average (Standard dev.)0.0024193982 (±0.046974123)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin9361044239
Dimensions1821401712
Spacing1401821712
CellA: 137.2 Å / B: 178.36 Å / C: 1677.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.980.980.98
M x/y/z1401821712
origin x/y/z0.0000.0000.000
length x/y/z137.200178.3601677.760
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS1044936239
NC/NR/NS1401821712
D min/max/mean-0.0713.2780.002

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Supplemental data

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Sample components

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Entire : Lethocerus flight muscle myosin filament

EntireName: Lethocerus flight muscle myosin filament
Components
  • Organelle or cellular component: Lethocerus flight muscle myosin filament
    • Protein or peptide: Myosin heavy chain isoform Mhc_X1

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Supramolecule #1: Lethocerus flight muscle myosin filament

SupramoleculeName: Lethocerus flight muscle myosin filament / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Details: The sample is a bipolar helical structure, with helical repeat 145 Angstrom and helical turn 33.98 degree. The sample has C4 symmetry. The map contains 6 unique features: myosin molecule ...Details: The sample is a bipolar helical structure, with helical repeat 145 Angstrom and helical turn 33.98 degree. The sample has C4 symmetry. The map contains 6 unique features: myosin molecule with completely resolved rods, 4 resolved non-myosin densities among the myosin rods and an annular region inside of annulus occupied by myosin rods that most likely contains paramyosin. The 4 non-myosin densities may contain parts of the proteins myofilin and flightin.
Source (natural)Organism: Lethocerus indicus (insect) / Organ: myocyte / Tissue: dorsal longitudinal indirect flight muscle / Organelle: Sarcomere / Location in cell: myofibril

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Macromolecule #1: Myosin heavy chain isoform Mhc_X1

MacromoleculeName: Myosin heavy chain isoform Mhc_X1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Lethocerus indicus (insect)
Molecular weightTheoretical: 225.227562 KDa
SequenceString: MPGSKPTKTE EEDDPTPYLF VSLEQKRIDQ TKPYDAKKAC WVPDEHEGFV QGEIRGTKGD IVSVHLPNGE TKDFKKDQVG QVNPPKFEK CEDMSNLTYL NDASVLYNLK QRYYNKLIYT YSGLFCVAIN PYKRFPVYTM RCAKLYRGKR RNEVPPHIFA I SDGAYVNM ...String:
MPGSKPTKTE EEDDPTPYLF VSLEQKRIDQ TKPYDAKKAC WVPDEHEGFV QGEIRGTKGD IVSVHLPNGE TKDFKKDQVG QVNPPKFEK CEDMSNLTYL NDASVLYNLK QRYYNKLIYT YSGLFCVAIN PYKRFPVYTM RCAKLYRGKR RNEVPPHIFA I SDGAYVNM LTNKENQSML ITGESGAGKT ENTKKVIAYF ATVGASTKKE EAASAASQKK GTLEDQVVQT NPVLEAFGNA KT VRNDNSS RFGKFIRIHF GPSGKLAGAD IETYLLEKAR VISQQSLERS YHIFYQVMSG AVPGVKELCL LSNDIYEYNY VSQ GKVTIP SVDDGEEFQA TDQAFDVLGF TQEEKDDIYK ITASVMHMGC MKFKQRGREE QAEADGTAEG ERVAKLLGLE AADL YKNLL KPRIKVGNEF VTQGRNLNQV IYSVGALSKG VFDRLFKFLV KKCNETLDTK QKRQHFIGVL DIAGFEIFDF NGFEQ LCIN FTNEKLQQFF NHHMFVLEQE EYTREGITWA FIDFGMDLVA CIDLIEKPMG ILSILEEESM FPKATDKTFE EKLMNN HLG KSPNFQKPKP PKPGCQAAHF AISHYAGVVS YNLTGWLEKN KDPLNDTVVD QFKKGSNKLL VEIFADHPGQ SGAPEAG GG GKGGRGKKGG GFATVSSSYK EQLNNLMTTL KSTQPHFVRC IIPNELKQPG LIDSHLVMHQ LTCNGVLEGI RICRKGFP N RMVYPDFKLR YMILAPATMA AEPDPKKAAD KCLKEVGLES ETYRIGHTKV FFRAGVLGQL EEMRDERLSK IIGWMQSHI RGYLARKQFK KYQDQRLSLQ VVQRNLRKYM ALRTWPWWKM WTKVKPLLNV ANVEEEMRKL EELVATTQAA LEKEEKARKE VEALNAKLI QEKTDLLRNL EGEKGSISSI QEKAAKLQAQ KSDLESQLMD TQERLQQEED NRNQMFQQKK KLEQEVGGLK K DIEDLELS LQKSDQDKAS KDHQIRNLND EIAHQDELIN KLNKEKKMQG EHTQKTAEEL QASEDKVNHL TKVKAKLEQT LD ELEDSLE REKKLRGDVE KAKRKVEGDL KLTQEAVADL ERNKKELEQT IQRKDKEIAS LTAKLEDEQS IVSKTQKQIK ELQ SRIEEL EEEVEAERQA RGKAEKQRAD LARELEELGE RLEEAGGATS AQIELNKKRE AEMSKLRRDL EESNIQHEST LANL RKKHN DAVSEMGEQI DQLNKLKTKA EHDRTHVQND LNNTRHALDQ MCREKAATEK IAKQLQHQVN EIQGKLDEAN RTLND FDSA KKKLSIENSD LLRQLEEAES QVSQLSKIKV SLTTQLEDTK RLADEEARER ATLLGKFRNL EHDLDNIREQ LEEEAE GKA DIQRQLSKAN AEAQLWRTKY ESEGVARAEE LEEAKRKLQA RLAEAEETIE SLNQKVIALE KTKQRLATEV EDLQLEV DR ATAIANAAEK KAKAIDKIIG EWKLKVDDLA AELDASQKEC RNYSTELFRL KGAYEEAQEQ LEAVRRENKN LADEVKDL L DQIGEGGRNI HEIEKQKKRL EVEKDELQAA LEEAEAALEQ EENKVLRSQL ELSQVRQEID RRIQEKEEEF ENTRKNHQR ALDSMQASLE AEAKGKAEAL RMKKKLEADI NELEIALDHA NKANSEAQKT IKKYQQQLKD VQTALEEEQR ARDDAREQLG ISERRANAL QNELEESRTL LEQADRGRRQ AEQELGDAHE QINELAAQAT SASAAKRKLE GELQTLHADL DELLNEAKNS E EKAKKAMV DAARLADELR AEQDHAQTQE KLRKALETQI KELQIRLDEA ETNALKGGKK AIAKLEQRVR ELENELDGEQ RR HADAQKN LRKSERRIKE LSFQADEDRK NHERMQDLVD KLQQKIKTYK RQIEEAEEIA ALNLAKFRKA QQELEEAEER ADL AEQAIA KFRTKGGRAG SAARAMSPVA HRPPVKHPLD GSTFPPRFDL HEDMM

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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
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
Image recordingFilm or detector model: DIRECT ELECTRON DE-64 (8k x 8k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 8192 pixel / Digitization - Dimensions - Height: 8192 pixel / Digitization - Frames/image: 1-34 / Number grids imaged: 1 / Number real images: 3507 / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf
Initial angle assignmentType: RANDOM ASSIGNMENT
Final 3D classificationNumber classes: 50
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 173515
FSC plot (resolution estimation)

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