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- EMDB-40933: Structure of mouse Myomaker bound to Fab18G7 in detergent -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-40933
TitleStructure of mouse Myomaker bound to Fab18G7 in detergent
Map data
Sample
  • Complex: Complex of mouse Myomaker and Fab18G7
    • Complex: Mouse Myomaker
      • Protein or peptide: Protein myomaker
    • Complex: Fab18G7
      • Protein or peptide: 18G7 Fab heavy chain
      • Protein or peptide: 18G7 Fab light chain
  • Ligand: ZINC ION
  • Ligand: CHOLESTEROL
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
  • Ligand: water
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


positive regulation of skeletal muscle hypertrophy / plasma membrane fusion / myoblast fusion involved in skeletal muscle regeneration / skeletal muscle tissue regeneration / myoblast fusion / muscle organ development / Golgi membrane / plasma membrane
Similarity search - Function
NGX6/PGAP6/MYMK / Protein of unknown function (DUF3522)
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.72 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-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40933.png

Downloads & links

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Map

FileDownload / File: emd_40933.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å

Surface

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Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-2.9051716 - 4.358551
Average (Standard dev.)0.0021148114 (±0.09353372)
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_40933_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_40933_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_40933_half_map_2.map
Projections & Slices
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Sample components

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Entire : Complex of mouse Myomaker and Fab18G7

EntireName: Complex of mouse Myomaker and Fab18G7
Components
  • Complex: Complex of mouse Myomaker and Fab18G7
    • Complex: Mouse Myomaker
      • Protein or peptide: Protein myomaker
    • Complex: Fab18G7
      • Protein or peptide: 18G7 Fab heavy chain
      • Protein or peptide: 18G7 Fab light chain
  • Ligand: ZINC ION
  • Ligand: CHOLESTEROL
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
  • Ligand: water

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Supramolecule #1: Complex of mouse Myomaker and Fab18G7

SupramoleculeName: Complex of mouse Myomaker and Fab18G7 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: Mouse Myomaker

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

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Supramolecule #3: Fab18G7

SupramoleculeName: Fab18G7 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Protein myomaker

MacromoleculeName: Protein myomaker / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.817469 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGTVVAKLLL PTLSSLAFLP TVSIATKRRF YMEAMVYLFT MFFVAFSHAC DGPGLSVLCF MRRDILEYFS IYGTALSMWV SLMALADFD EPQRSTFTML GVLTIAVRTF HDRWGYGVYS GPIGTATLII AVKWLKKMKE KKGLYPDKSI YTQQIGPGLC F GALALMLR ...String:
MGTVVAKLLL PTLSSLAFLP TVSIATKRRF YMEAMVYLFT MFFVAFSHAC DGPGLSVLCF MRRDILEYFS IYGTALSMWV SLMALADFD EPQRSTFTML GVLTIAVRTF HDRWGYGVYS GPIGTATLII AVKWLKKMKE KKGLYPDKSI YTQQIGPGLC F GALALMLR FFFEEWDYTY VHSFYHCALA MSFVLLLPKV NKKAGNAGAP AKLTFSTLCC TCV

UniProtKB: Protein myomaker

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Macromolecule #2: 18G7 Fab heavy chain

MacromoleculeName: 18G7 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.318994 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVTLKESGPG ILQPSQTLSL TCSFSGFSLS TSGMGVSWIR KPSGKGLEWL AHIFWDDDKR YNPSLKSRLT ISKDTSSNQV FLMITSIDT ADTATYYCAR RTWLLHAMDY WGQGTSVTVS S

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Macromolecule #3: 18G7 Fab light chain

MacromoleculeName: 18G7 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.809201 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPSS LSASLGGKVT ITCKASQDIN EYIAWYQHKP GKGPRLLIHY TSTLQPGIPS RFSGSGSGRD YSFSISNLEP EDIATYYCL QYDNLLWTFG GGTKLEIK

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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

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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

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 371611
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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