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- PDB-8t05: Structure of Ciona Myomaker bound to Fab1A1 -

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Basic information

Entry
Database: PDB / ID: 8t05
TitleStructure of Ciona Myomaker bound to Fab1A1
Components
  • 1A1 Fab heavy chain
  • 1A1 Fab light chain
  • Myomaker
KeywordsMEMBRANE PROTEIN
Function / homologyCHOLESTEROL / 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
Function and homology information
Biological speciesCiona robusta (invertebrata)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsLong, T. / Li, X.
Funding support United States, 1items
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, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Database references / Category: citation_author
Revision 1.2Oct 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Nov 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Feb 14, 2024Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.5Feb 21, 2024Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.6Nov 13, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myomaker
B: Myomaker
C: 1A1 Fab heavy chain
D: 1A1 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,44910
Polymers74,0244
Non-polymers2,4246
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Myomaker


Mass: 24407.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ciona robusta (invertebrata) / Production host: Spodoptera frugiperda (fall armyworm)

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Antibody , 2 types, 2 molecules CD

#2: Antibody 1A1 Fab heavy chain


Mass: 13419.872 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody 1A1 Fab light chain


Mass: 11790.040 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Non-polymers , 3 types, 6 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O
#6: Chemical ChemComp-LBN / 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / (2R)-2-[(9Z)-9-Octadecenoyloxy]-3-(palmitoyloxy)propyl 2-(trimethylammonio)ethyl phosphate


Mass: 760.076 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H82NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Complex of Ciona robusta Myomaker with Fab1A1COMPLEX#1-#30MULTIPLE SOURCES
2Ciona robusta MyomakerCOMPLEX#11RECOMBINANT
3Fab1A1COMPLEX#2-#31NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Ciona robusta (invertebrata)1774208
33Mus musculus (house mouse)10090
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Spodoptera frugiperda (fall armyworm)7108
33Homo sapiens (human)9606
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: REFMAC / Version: 5.8.0267 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 145594 / Symmetry type: POINT
RefinementResolution: 3.22→249 Å / Cor.coef. Fo:Fc: 0.754 / Cor.coef. Fo:Fc free: 0.754 / SU B: 11.407 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.45086 50773 5.2 %RANDOM
Rwork0.4488 ---
obs0.44891 917698 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 110.417 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20.95 Å21.87 Å2
2--0.35 Å2-1.04 Å2
3----0.34 Å2
Refinement stepCycle: 1 / Total: 5104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0030.0135241
ELECTRON MICROSCOPYr_bond_other_d0.0010.0155097
ELECTRON MICROSCOPYr_angle_refined_deg1.3751.6677113
ELECTRON MICROSCOPYr_angle_other_deg1.1111.6311729
ELECTRON MICROSCOPYr_dihedral_angle_1_deg8.2385627
ELECTRON MICROSCOPYr_dihedral_angle_2_deg33.12521.848211
ELECTRON MICROSCOPYr_dihedral_angle_3_deg13.49915842
ELECTRON MICROSCOPYr_dihedral_angle_4_deg12.3281518
ELECTRON MICROSCOPYr_chiral_restr0.0710.2681
ELECTRON MICROSCOPYr_gen_planes_refined0.0040.025674
ELECTRON MICROSCOPYr_gen_planes_other0.0020.021226
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it1.32911.7732520
ELECTRON MICROSCOPYr_mcbond_other1.3311.7712519
ELECTRON MICROSCOPYr_mcangle_it2.50417.6543143
ELECTRON MICROSCOPYr_mcangle_other2.50417.6553144
ELECTRON MICROSCOPYr_scbond_it0.72811.9242721
ELECTRON MICROSCOPYr_scbond_other0.72811.9252721
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other1.46717.8453970
ELECTRON MICROSCOPYr_long_range_B_refined4.8635663
ELECTRON MICROSCOPYr_long_range_B_other4.8635664
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.22→3.304 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree2.21 4104 -
Rwork2.223 67684 -
obs--100 %

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