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- PDB-7usw: Structure of Expanded C. elegans TMC-1 complex -

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Basic information

Entry
Database: PDB / ID: 7usw
TitleStructure of Expanded C. elegans TMC-1 complex
Components
  • (Transmembrane ...) x 2
  • CALMyrin (Calcium and Integrin Binding protein) homolog
KeywordsMEMBRANE PROTEIN / Complex
Function / homology
Function and homology information


detection of stimulus involved in sensory perception / striated muscle dense body / mechanosensitive monoatomic ion channel activity / sensory perception of chemical stimulus / sodium channel activity / non-motile cilium / calcium ion homeostasis / monoatomic ion transmembrane transport / monoatomic ion channel activity / neuronal cell body ...detection of stimulus involved in sensory perception / striated muscle dense body / mechanosensitive monoatomic ion channel activity / sensory perception of chemical stimulus / sodium channel activity / non-motile cilium / calcium ion homeostasis / monoatomic ion transmembrane transport / monoatomic ion channel activity / neuronal cell body / calcium ion binding / magnesium ion binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Transmembrane inner ear expressed protein / TMIE protein / TMC domain / Transmembrane channel-like protein / TMC domain / EF-hand domain pair / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / CHOLESTEROL / DODECANE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / PALMITIC ACID / HEXADECANE / undecan-1-ol / Transmembrane channel-like protein 1 / EF-hand domain-containing protein / Transmembrane inner ear
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsJeong, H. / Clark, S. / Gouaux, E.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2022
Title: Structures of the TMC-1 complex illuminate mechanosensory transduction.
Authors: Hanbin Jeong / Sarah Clark / April Goehring / Sepehr Dehghani-Ghahnaviyeh / Ali Rasouli / Emad Tajkhorshid / Eric Gouaux /
Abstract: The initial step in the sensory transduction pathway underpinning hearing and balance in mammals involves the conversion of force into the gating of a mechanosensory transduction channel. Despite the ...The initial step in the sensory transduction pathway underpinning hearing and balance in mammals involves the conversion of force into the gating of a mechanosensory transduction channel. Despite the profound socioeconomic impacts of hearing disorders and the fundamental biological significance of understanding mechanosensory transduction, the composition, structure and mechanism of the mechanosensory transduction complex have remained poorly characterized. Here we report the single-particle cryo-electron microscopy structure of the native transmembrane channel-like protein 1 (TMC-1) mechanosensory transduction complex isolated from Caenorhabditis elegans. The two-fold symmetric complex is composed of two copies each of the pore-forming TMC-1 subunit, the calcium-binding protein CALM-1 and the transmembrane inner ear protein TMIE. CALM-1 makes extensive contacts with the cytoplasmic face of the TMC-1 subunits, whereas the single-pass TMIE subunits reside on the periphery of the complex, poised like the handles of an accordion. A subset of complexes additionally includes a single arrestin-like protein, arrestin domain protein (ARRD-6), bound to a CALM-1 subunit. Single-particle reconstructions and molecular dynamics simulations show how the mechanosensory transduction complex deforms the membrane bilayer and suggest crucial roles for lipid-protein interactions in the mechanism by which mechanical force is transduced to ion channel gating.
History
DepositionApr 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 2.0Oct 26, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / citation_author / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.auth_comp_id ..._atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id
Revision 2.1Nov 9, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 3.0Aug 9, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Data processing / Derived calculations / Refinement description / Structure summary
Category: atom_site / em_3d_reconstruction ...atom_site / em_3d_reconstruction / em_ctf_correction / em_image_processing / em_image_recording / em_software / entity / pdbx_contact_author / pdbx_entity_instance_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / refine / software / struct_asym / struct_conn
Item: _entity.pdbx_number_of_molecules / _pdbx_poly_seq_scheme.auth_mon_id ..._entity.pdbx_number_of_molecules / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _refine.ls_d_res_high
Description: Model completeness / Details: Palmitoylation of TMIE C43 / Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transmembrane channel-like protein 1
B: Transmembrane channel-like protein 1
C: CALMyrin (Calcium and Integrin Binding protein) homolog
D: Transmembrane inner ear expressed protein
E: CALMyrin (Calcium and Integrin Binding protein) homolog
F: Transmembrane inner ear expressed protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)381,49376
Polymers367,1386
Non-polymers14,35470
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Transmembrane ... , 2 types, 4 molecules ABDF

#1: Protein Transmembrane channel-like protein 1


Mass: 147331.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: D3KZG3
#3: Protein Transmembrane inner ear expressed protein


Mass: 12668.813 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q9XXE7

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Protein / Sugars , 2 types, 4 molecules CE

#11: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#2: Protein CALMyrin (Calcium and Integrin Binding protein) homolog


Mass: 23568.568 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q93640

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Non-polymers , 8 types, 68 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 744.034 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H78NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: DOPE, phospholipid*YM
#6: Chemical ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H82NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#7: Chemical...
ChemComp-ZFC / undecan-1-ol


Mass: 172.308 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: C11H24O / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: C12H26 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical
ChemComp-R16 / HEXADECANE


Mass: 226.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H34 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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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

ComponentName: Native TMC-1 complex / Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL
Molecular weightValue: 0.43 MDa / Experimental value: YES
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Buffer solutionpH: 8.5
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: 2400 nm / Nominal defocus min: 1000 nm
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
1150GATAN K3 BIOQUANTUM (6k x 4k)
2150GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

Image processing
IDImage recording-ID
11
21
31
CTF correction
IDEM image processing-IDType
11PHASE FLIPPING AND AMPLITUDE CORRECTION
22PHASE FLIPPING AND AMPLITUDE CORRECTION
33PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstruction
IDResolution (Å)Resolution methodNum. of particlesImage processing-IDEntry-IDSymmetry type
13.1FSC 0.143 CUT-OFF14239617USWPOINT
23.1FSC 0.143 CUT-OFF14239617USWPOINT
33.1FSC 0.143 CUT-OFF14239617USWPOINT
43.1FSC 0.143 CUT-OFF14239627USWPOINT
53.1FSC 0.143 CUT-OFF14239627USWPOINT
63.1FSC 0.143 CUT-OFF14239627USWPOINT
73.1FSC 0.143 CUT-OFF14239637USWPOINT
83.1FSC 0.143 CUT-OFF14239637USWPOINT
93.1FSC 0.143 CUT-OFF14239637USWPOINT
RefinementHighest resolution: 3.1 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00314576
ELECTRON MICROSCOPYf_angle_d0.48819494
ELECTRON MICROSCOPYf_dihedral_angle_d6.5952344
ELECTRON MICROSCOPYf_chiral_restr0.0382156
ELECTRON MICROSCOPYf_plane_restr0.0042342

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