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- EMDB-40935: Structure of Ciona Myomaker bound to Fab1A1 -

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Basic information

Entry
Database: EMDB / ID: EMD-40935
TitleStructure of Ciona Myomaker bound to Fab1A1
Map data
Sample
  • Complex: Complex of Ciona robusta Myomaker with Fab1A1
    • Complex: Ciona robusta Myomaker
      • Protein or peptide: Myomaker
    • Complex: Fab1A1
      • Protein or peptide: 1A1 Fab heavy chain
      • Protein or peptide: 1A1 Fab light chain
  • Ligand: ZINC ION
  • Ligand: CHOLESTEROL
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
KeywordsMEMBRANE PROTEIN
Biological speciesCiona robusta (invertebrata) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsLong T / Li X
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM135343 United States
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: Cryo-EM structures of Myomaker reveal a molecular basis for myoblast fusion.
Authors: Tao Long / Yichi Zhang / Linda Donnelly / Hui Li / Yu-Chung Pien / Ning Liu / Eric N Olson / Xiaochun Li /
Abstract: The fusion of mononucleated myoblasts produces multinucleated muscle fibers leading to the formation of skeletal muscle. Myomaker, a skeletal muscle-specific membrane protein, is essential for ...The fusion of mononucleated myoblasts produces multinucleated muscle fibers leading to the formation of skeletal muscle. Myomaker, a skeletal muscle-specific membrane protein, is essential for myoblast fusion. Here we report the cryo-EM structures of mouse Myomaker (mMymk) and Ciona robusta Myomaker (cMymk). Myomaker contains seven transmembrane helices (TMs) that adopt a G-protein-coupled receptor-like fold. TMs 2-4 form a dimeric interface, while TMs 3 and 5-7 create a lipid-binding site that holds the polar head of a phospholipid and allows the alkyl tails to insert into Myomaker. The similarity of cMymk and mMymk suggests a conserved Myomaker-mediated cell fusion mechanism across evolutionarily distant species. Functional analyses demonstrate the essentiality of the dimeric interface and the lipid-binding site for fusogenic activity, and heterologous cell-cell fusion assays show the importance of transcellular interactions of Myomaker protomers for myoblast fusion. Together, our findings provide structural and functional insights into the process of myoblast fusion.
History
DepositionMay 31, 2023-
Header (metadata) releaseSep 27, 2023-
Map releaseSep 27, 2023-
UpdateFeb 21, 2024-
Current statusFeb 21, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40935.png

Downloads & links

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Map

FileDownload / File: emd_40935.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-2.6438248 - 3.7006567
Average (Standard dev.)0.004036836 (±0.06570858)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_40935_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_40935_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_40935_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of Ciona robusta Myomaker with Fab1A1

EntireName: Complex of Ciona robusta Myomaker with Fab1A1
Components
  • Complex: Complex of Ciona robusta Myomaker with Fab1A1
    • Complex: Ciona robusta Myomaker
      • Protein or peptide: Myomaker
    • Complex: Fab1A1
      • Protein or peptide: 1A1 Fab heavy chain
      • Protein or peptide: 1A1 Fab light chain
  • Ligand: ZINC ION
  • Ligand: CHOLESTEROL
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine

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Supramolecule #1: Complex of Ciona robusta Myomaker with Fab1A1

SupramoleculeName: Complex of Ciona robusta Myomaker with Fab1A1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: Ciona robusta Myomaker

SupramoleculeName: Ciona robusta Myomaker / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Ciona robusta (invertebrata)

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Supramolecule #3: Fab1A1

SupramoleculeName: Fab1A1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Myomaker

MacromoleculeName: Myomaker / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Ciona robusta (invertebrata)
Molecular weightTheoretical: 24.407203 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGLILVKFLL PAISSGAFFI PGIFATKKRL FTLAFLYIFT AFFQLFFHLC TTPLLSLLFC LMGKKLLTFF STYGLVLSIY STLTQLTRY TDDRKHSAVV CGGLLIGVRI FQENEGPGVY AGPLITGGLL LAISWGQEMY RSKALYPDKE KWLKIILPSF A LGAVSLLL ...String:
MGLILVKFLL PAISSGAFFI PGIFATKKRL FTLAFLYIFT AFFQLFFHLC TTPLLSLLFC LMGKKLLTFF STYGLVLSIY STLTQLTRY TDDRKHSAVV CGGLLIGVRI FQENEGPGVY AGPLITGGLL LAISWGQEMY RSKALYPDKE KWLKIILPSF A LGAVSLLL LCVFQNSWNY AFVHSIHHLL MSAAITIILR LVEDGEKQDK CCGLSIACCI C

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Macromolecule #2: 1A1 Fab heavy chain

MacromoleculeName: 1A1 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.419872 KDa
SequenceString:
QAYLQQSGAE LVRPGASVKM SCKASGYTFT SYNMHWVKQT PRQGLEWIGA IYPGNGESSN NQKFKGKATL TVDKSSNTAY MQLSSLTSE DSAVYFCARG EGNYFRSGWF AYWGQGTLVT VSS

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Macromolecule #3: 1A1 Fab light chain

MacromoleculeName: 1A1 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.79004 KDa
SequenceString:
DIVMTQSPAS LSVPVGETVT ITCRTSENIY SNLAWYQQKQ GKSPQLLVYA ATNLADGVPS RFSGSGSGTQ YSLKINSLQS EDFGSYYCQ HFWSTPWTFG EGTKLEIK

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #5: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 5 / Number of copies: 2 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL / Cholesterol

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Macromolecule #6: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine

MacromoleculeName: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / type: ligand / ID: 6 / Number of copies: 2 / Formula: LBN
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-LBN:
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / phospholipid*YM / POPC

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
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: 1.8 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 145594

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