[English] 日本語
Yorodumi
- PDB-7usy: Structure of C. elegans TMC-1 complex with ARRD-6 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7usy
TitleStructure of C. elegans TMC-1 complex with ARRD-6
Components
  • (Transmembrane ...Transmembrane protein) x 2
  • ARRestin Domain protein
  • 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 / sensory perception of chemical stimulus / mechanosensitive monoatomic ion channel activity / non-motile cilium / sodium channel activity / calcium ion homeostasis / monoatomic ion transmembrane transport / protein transport / monoatomic ion channel activity ...detection of stimulus involved in sensory perception / striated muscle dense body / sensory perception of chemical stimulus / mechanosensitive monoatomic ion channel activity / non-motile cilium / sodium channel activity / calcium ion homeostasis / monoatomic ion transmembrane transport / protein 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 / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain ...Transmembrane inner ear expressed protein / TMIE protein / TMC domain / Transmembrane channel-like protein / TMC domain / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin-like, C-terminal / EF-hand domain pair / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Immunoglobulin E-set
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / PALMITIC ACID / ARRestin Domain protein / 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: 3.54 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 / pdbx_validate_close_contact / 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 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_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 / pdbx_validate_close_contact / refine / software / struct_asym / struct_conn
Item: _em_image_recording.avg_electron_dose_per_image / _entity.pdbx_number_of_molecules ..._em_image_recording.avg_electron_dose_per_image / _entity.pdbx_number_of_molecules / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
J: ARRestin Domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)425,01525
Polymers420,2427
Non-polymers4,77318
Water0
1


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

-
Components

-
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

-
Protein , 2 types, 3 molecules CEJ

#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
#4: Protein ARRestin Domain protein


Mass: 53103.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: D1MN74

-
Sugars , 1 types, 2 molecules

#8: 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 / N-Acetylglucosamine


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

-
Non-polymers , 4 types, 16 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


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


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


Mass: 748.065 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H82NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#9: Chemical
ChemComp-PLM / PALMITIC ACID / Palmitic acid


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

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Native TMC-1 complex / Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL
Molecular weightValue: 0.48 MDa / Experimental value: NO
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

-
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 FIELDBright-field microscopy / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

Image processing
IDImage recording-ID
11
21
CTF correction
IDEM image processing-IDType
11PHASE FLIPPING AND AMPLITUDE CORRECTION
22PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstruction
IDResolution (Å)Resolution methodNum. of particlesImage processing-IDEntry-IDSymmetry type
13.54FSC 0.143 CUT-OFF9924817USYPOINT
23.54FSC 0.143 CUT-OFF9924817USYPOINT
33.54FSC 0.143 CUT-OFF9924827USYPOINT
43.54FSC 0.143 CUT-OFF9924827USYPOINT
RefinementHighest resolution: 3.54 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00317514
ELECTRON MICROSCOPYf_angle_d0.64723473
ELECTRON MICROSCOPYf_dihedral_angle_d7.4182746
ELECTRON MICROSCOPYf_chiral_restr0.042602
ELECTRON MICROSCOPYf_plane_restr0.0072855

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more