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- EMDB-12289: Structure of the in situ actomyosin complex from the A-band of mo... -

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Entry
Database: EMDB / ID: EMD-12289
TitleStructure of the in situ actomyosin complex from the A-band of mouse psoas muscle sarcomere in the rigor state obtained by sub-tomogram averaging
Map dataAveraged map of in situ actomyosin complex
Sample
  • Complex: In situ actomyosin complex in the rigor state from mouse psoas muscle
    • Complex: actin
      • Protein or peptide: Actin, alpha skeletal muscle
    • Complex: myosin double head
      • Protein or peptide: Myosin-4
      • Protein or peptide: Myosin light chain 1/3, skeletal muscle isoform
      • Protein or peptide: Myosin regulatory light chain 2, skeletal muscle isoform
    • Complex: tropomyosin
      • Protein or peptide: Tropomyosin alpha-1 chain
KeywordsMuscle proteins / force generation / sarcomere / cytoskeleton / MOTOR PROTEIN
Function / homology
Function and homology information


positive regulation of heart rate by epinephrine / muscle thin filament tropomyosin / Formation of the dystrophin-glycoprotein complex (DGC) / Striated Muscle Contraction / Smooth Muscle Contraction / muscle myosin complex / myosin filament / myosin complex / structural constituent of muscle / ventricular cardiac muscle tissue morphogenesis ...positive regulation of heart rate by epinephrine / muscle thin filament tropomyosin / Formation of the dystrophin-glycoprotein complex (DGC) / Striated Muscle Contraction / Smooth Muscle Contraction / muscle myosin complex / myosin filament / myosin complex / structural constituent of muscle / ventricular cardiac muscle tissue morphogenesis / response to muscle activity / myofibril / mesenchyme migration / cytoskeletal motor activity / striated muscle thin filament / skeletal muscle thin filament assembly / skeletal muscle tissue development / skeletal muscle fiber development / stress fiber / cardiac muscle contraction / muscle contraction / actin filament / filopodium / structural constituent of cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin filament binding / actin cytoskeleton / lamellipodium / double-stranded RNA binding / cell body / in utero embryonic development / calmodulin binding / hydrolase activity / protein heterodimerization activity / calcium ion binding / positive regulation of gene expression / protein homodimerization activity / protein-containing complex / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
: / EF-hand domain / Tropomyosins signature. / Tropomyosin / Tropomyosin / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal ...: / EF-hand domain / Tropomyosins signature. / Tropomyosin / Tropomyosin / 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 / Actins signature 1. / Actin, conserved site / : / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / EF-hand, calcium binding motif / ATPase, nucleotide binding domain / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Myosin light chain 1/3, skeletal muscle isoform / Tropomyosin alpha-1 chain / Actin, alpha skeletal muscle / Myosin regulatory light chain 11 / Myosin-4
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 10.2 Å
AuthorsWang Z / Grange M
Funding support Germany, United Kingdom, European Union, 5 items
OrganizationGrant numberCountry
Max Planck Society Germany
Wellcome Trust201543/Z/16/Z United Kingdom
European Research Council (ERC)856118European Union
Medical Research Council (MRC, United Kingdom)MR/R003106/1 United Kingdom
European Molecular Biology Organization (EMBO)ALTF 693-2018European Union
CitationJournal: Cell / Year: 2021
Title: The molecular basis for sarcomere organization in vertebrate skeletal muscle.
Authors: Zhexin Wang / Michael Grange / Thorsten Wagner / Ay Lin Kho / Mathias Gautel / Stefan Raunser /
Abstract: Sarcomeres are force-generating and load-bearing devices of muscles. A precise molecular picture of how sarcomeres are built underpins understanding their role in health and disease. Here, we ...Sarcomeres are force-generating and load-bearing devices of muscles. A precise molecular picture of how sarcomeres are built underpins understanding their role in health and disease. Here, we determine the molecular architecture of native vertebrate skeletal sarcomeres by electron cryo-tomography. Our reconstruction reveals molecular details of the three-dimensional organization and interaction of actin and myosin in the A-band, I-band, and Z-disc and demonstrates that α-actinin cross-links antiparallel actin filaments by forming doublets with 6-nm spacing. Structures of myosin, tropomyosin, and actin at ~10 Å further reveal two conformations of the "double-head" myosin, where the flexible orientation of the lever arm and light chains enable myosin not only to interact with the same actin filament, but also to split between two actin filaments. Our results provide unexpected insights into the fundamental organization of vertebrate skeletal muscle and serve as a strong foundation for future investigations of muscle diseases.
History
DepositionFeb 4, 2021-
Header (metadata) releaseApr 7, 2021-
Map releaseApr 7, 2021-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
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  • Surface view colored by cylindrical radius
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  • Surface view with fitted model
  • Atomic models: PDB-7nep
  • Surface level: 0.02
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7nep
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12289.png

Downloads & links

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Map

FileDownload / File: emd_12289.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAveraged map of in situ actomyosin complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.76 Å/pix.
x 200 pix.
= 351. Å		1.76 Å/pix.
x 200 pix.
= 351. Å		1.76 Å/pix.
x 200 pix.
= 351. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.755 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.02
Minimum - Maximum-0.06538552 - 0.099714175
Average (Standard dev.)0.0005608661 (±0.0068937363)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 351.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.7551.7551.755
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z351.000351.000351.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ160160160
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0650.1000.001

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Supplemental data

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Mask #1

Fileemd_12289_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_12289_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_12289_half_map_2.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : In situ actomyosin complex in the rigor state from mouse psoas muscle

EntireName: In situ actomyosin complex in the rigor state from mouse psoas muscle
Components
  • Complex: In situ actomyosin complex in the rigor state from mouse psoas muscle
    • Complex: actin
      • Protein or peptide: Actin, alpha skeletal muscle
    • Complex: myosin double head
      • Protein or peptide: Myosin-4
      • Protein or peptide: Myosin light chain 1/3, skeletal muscle isoform
      • Protein or peptide: Myosin regulatory light chain 2, skeletal muscle isoform
    • Complex: tropomyosin
      • Protein or peptide: Tropomyosin alpha-1 chain

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Supramolecule #1: In situ actomyosin complex in the rigor state from mouse psoas muscle

SupramoleculeName: In situ actomyosin complex in the rigor state from mouse psoas muscle
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #2: actin

SupramoleculeName: actin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #3: myosin double head

SupramoleculeName: myosin double head / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#5
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #4: tropomyosin

SupramoleculeName: tropomyosin / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 41.747527 KDa
SequenceString: EDETTALVCD NGSGLVKAGF AGDDAPRAVF PSIVGRPRHQ GVMVGMGQKD SYVGDEAQSK RGILTLKYPI EHGIITNWDD MEKIWHHTF YNELRVAPEE HPTLLTEAPL NPKANREKMT QIMFETFNVP AMYVAIQAVL SLYASGRTTG IVLDSGDGVT H NVPIYEGY ...String:
EDETTALVCD NGSGLVKAGF AGDDAPRAVF PSIVGRPRHQ GVMVGMGQKD SYVGDEAQSK RGILTLKYPI EHGIITNWDD MEKIWHHTF YNELRVAPEE HPTLLTEAPL NPKANREKMT QIMFETFNVP AMYVAIQAVL SLYASGRTTG IVLDSGDGVT H NVPIYEGY ALPHAIMRLD LAGRDLTDYL MKILTERGYS FVTTAEREIV RDIKEKLCYV ALDFENEMAT AASSSSLEKS YE LPDGQVI TIGNERFRCP ETLFQPSFIG MESAGIHETT YNSIMKCDID IRKDLYANNV MSGGTTMYPG IADRMQKEIT ALA PSTMKI KIIAPPERKY SVWIGGSILA SLSTFQQMWI TKQEYDEAGP SIVHRKCF

UniProtKB: Actin, alpha skeletal muscle

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Macromolecule #2: Tropomyosin alpha-1 chain

MacromoleculeName: Tropomyosin alpha-1 chain / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 28.922074 KDa
SequenceString: LKLDKENALD RAEQAEADKK AAEDRSKQLE DELVSLQKKL KGTEDELDKY SEALKDAQEK LELAEKKATD AEADVASLNR RIQLVEEEL DRAQERLATA LQKLEEAEKA ADESERGMKV IESRAQKDEE KMEIQEIQLK EAKHIAEDAD RKYEEVARKL V IIESDLER ...String:
LKLDKENALD RAEQAEADKK AAEDRSKQLE DELVSLQKKL KGTEDELDKY SEALKDAQEK LELAEKKATD AEADVASLNR RIQLVEEEL DRAQERLATA LQKLEEAEKA ADESERGMKV IESRAQKDEE KMEIQEIQLK EAKHIAEDAD RKYEEVARKL V IIESDLER AEERAELSEG KCAELEEELK TVTNNLKSLE AQAEKYSQKE DKYEEEIKVL SDKLKEAETR AEFAERSVTK LE KSIDDLE DELY

UniProtKB: Tropomyosin alpha-1 chain

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Macromolecule #3: Myosin-4

MacromoleculeName: Myosin-4 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 92.518234 KDa
SequenceString: FDAKSSVFVV DAKESYVKAT VQSREGGKVT AKTEGGATVT VKDDQVFSMN PPKYDKIEDM AMMTHLHEPA VLYNLKERYA AWMIYTYSG LFCVTVNPYK WLPVYNPEVV AAYRGKKRQE APPHIFSISD NAYQFMLTDR ENQSILITGE SGAGKTVNTK R VIQYFATI ...String:
FDAKSSVFVV DAKESYVKAT VQSREGGKVT AKTEGGATVT VKDDQVFSMN PPKYDKIEDM AMMTHLHEPA VLYNLKERYA AWMIYTYSG LFCVTVNPYK WLPVYNPEVV AAYRGKKRQE APPHIFSISD NAYQFMLTDR ENQSILITGE SGAGKTVNTK R VIQYFATI AVTGDKKKEE ATSGKMQGTL EDQIISANPL LEAFGNAKTV RNDNSSRFGK FIRIHFGATG KLASADIETY LL EKSRVTF QLKAERSYHI FYQIMSNKKP ELIEMLLITT NPYDFAYVSQ GEITVPSIDD QEELMATDTA VDILGFSADE KVA IYKLTG AVMHYGNMKF KQKQREEQAE PDGTEVADKA AYLTSLNSAD LLKALCYPRV KVGNEYVTKG QTVQQVYNSV GALA KSMYE KMFLWMVTRI NQQLDTKQPR QYFIGVLDIA GFEIFDFNTL EQLCINFTNE KLQQFFNHHM FVLEQEEYKK EGIDW EFID FGMDLAACIE LIEKPMGIFS ILEEECMFPK ATDTSFKNKL YEQHLGKSNN FQKPKPAKGK AEAHFSLVHY AGTVDY NII GWLDKNKDPL NETVVGLYQK SGLKTLAFLF SGGQAAEAEG GGGKKGGKKK GSSFQTVSAL FRENLNKLMT NLKSTHP HF VRCLIPNETK TPGAMEHELV LHQLRCNGVL EGIRICRKGF PSRILYADFK QRYKVLNASA IPEGQFIDSK KASEKLLG S IDIDHTQYKF GHTKVFFKAG LLGTLEEMRD EKLAQLITRT QAVCRGYLMR VEFKKMMERR ESIFCIQYNV RAFMNVKHW PWMKLYFKIK PLL

UniProtKB: Myosin-4

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Macromolecule #4: Myosin light chain 1/3, skeletal muscle isoform

MacromoleculeName: Myosin light chain 1/3, skeletal muscle isoform / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 16.57359 KDa
SequenceString:
EFSKEQQEDF KEAFLLFDRT GECKITLSQV GDVLRALGTN PTNAEVKKVL GNPSNEEMNA KKIEFEQFLP MMQAISNNKD QGGYEDFVE GLRVFDKEGN GTVMGAELRH VLATLGEKMK EEEVEALLAG QEDSNGCINY EAFVKHIMS

UniProtKB: Myosin light chain 1/3, skeletal muscle isoform

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Macromolecule #5: Myosin regulatory light chain 2, skeletal muscle isoform

MacromoleculeName: Myosin regulatory light chain 2, skeletal muscle isoform
type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 16.326439 KDa
SequenceString:
MFDQTQIQEF KEAFTVIDQN RDGIIDKEDL RDTFAAMGRL NVKNEELDAM MKEASGPINF TVFLTMFGEK LKGADPEDVI TGAFKVLDP EGKGTIKKQF LEELLTTQCD RFSQEEIKNM WAAFPPDVGG NVDYKNICYV ITHGD

UniProtKB: Myosin regulatory light chain 11

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
140.0 mMKClpotassium chloride
2.0 mMMgCl2magnesium chloride
1.0 mMEGTAegtazic acid
1.0 mMDTTdithiothreitol
GridModel: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 286 K / Instrument: FEI VITROBOT MARK IV
DetailsThe sample was myofibrils.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 1-8 / Average electron dose: 3.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 28409 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 10.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.4) / Number subtomograms used: 18090
ExtractionNumber tomograms: 8 / Number images used: 32421
Final 3D classificationSoftware - Name: RELION (ver. 3.0.4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

5jlh

source_name: PDB, initial_model_type: experimental model

6kn8

source_name: PDB, initial_model_type: experimental model

3i5g

source_name: PDB, initial_model_type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-7nep:
Homology model of the in situ actomyosin complex from the A-band of mouse psoas muscle sarcomere in the rigor state

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