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- EMDB-41356: Structure of the C. elegans TMC-2 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-41356
TitleStructure of the C. elegans TMC-2 complex
Map dataStructure of the C. elegans TMC-2 complex
Sample
  • Complex: C. elegans TMC-2 complex
    • Protein or peptide: Transmembrane channel-like protein 2
    • Protein or peptide: CALMyrin (Calcium and Integrin Binding protein) homolog
    • Protein or peptide: Transmembrane inner ear expressed protein
  • Ligand: DOCOSANE
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: HEXADECANE
  • Ligand: CHOLESTEROL
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
  • Ligand: PALMITIC ACID
KeywordsMechanosensory transduction Macromolecular complex / MEMBRANE PROTEIN
Function / homology
Function and homology information


striated muscle dense body / mechanosensitive monoatomic ion channel activity / calcium ion homeostasis / 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
Transmembrane channel-like protein 2 / EF-hand domain-containing protein / Transmembrane inner ear
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsClark S / Jeong H / Goehring A / Posert R / Gouaux E
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: The structure of the TMC-2 complex suggests roles of lipid-mediated subunit contacts in mechanosensory transduction.
Authors: Sarah Clark / Hanbin Jeong / Rich Posert / April Goehring / Eric Gouaux /
Abstract: Mechanotransduction is the process by which a mechanical force, such as touch, is converted into an electrical signal. Transmembrane channel-like (TMC) proteins are an evolutionarily conserved family ...Mechanotransduction is the process by which a mechanical force, such as touch, is converted into an electrical signal. Transmembrane channel-like (TMC) proteins are an evolutionarily conserved family of membrane proteins whose function has been linked to a variety of mechanosensory processes, including hearing and balance sensation in vertebrates and locomotion in . TMC1 and TMC2 are components of ion channel complexes, but the molecular features that tune these complexes to diverse mechanical stimuli are unknown. express two TMC homologs, TMC-1 and TMC-2, both of which are the likely pore-forming subunits of mechanosensitive ion channels but differ in their expression pattern and functional role in the worm. Here, we present the single-particle cryo-electron microscopy structure of the native TMC-2 complex isolated from . The complex is composed of two copies of the pore-forming TMC-2 subunit, the calcium and integrin binding protein CALM-1 and the transmembrane inner ear protein TMIE. Comparison of the TMC-2 complex to the recently published cryo-EM structure of the TMC-1 complex highlights conserved protein-lipid interactions, as well as a π-helical structural motif in the pore-forming helices, that together suggest a mechanism for TMC-mediated mechanosensory transduction.
History
DepositionJul 25, 2023-
Header (metadata) releaseMar 27, 2024-
Map releaseMar 27, 2024-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41356.png

Downloads & links

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Map

FileDownload / File: emd_41356.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the C. elegans TMC-2 complex
Voxel sizeX=Y=Z: 0.831 Å
Density
Contour LevelBy AUTHOR: 0.075
Minimum - Maximum-0.24394153 - 0.53618604
Average (Standard dev.)0.0005113131 (±0.009068123)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 373.94998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Additional Map

Fileemd_41356_additional_1.map
AnnotationAdditional Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 1

Fileemd_41356_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_41356_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : C. elegans TMC-2 complex

EntireName: C. elegans TMC-2 complex
Components
  • Complex: C. elegans TMC-2 complex
    • Protein or peptide: Transmembrane channel-like protein 2
    • Protein or peptide: CALMyrin (Calcium and Integrin Binding protein) homolog
    • Protein or peptide: Transmembrane inner ear expressed protein
  • Ligand: DOCOSANE
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: HEXADECANE
  • Ligand: CHOLESTEROL
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
  • Ligand: PALMITIC ACID

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Supramolecule #1: C. elegans TMC-2 complex

SupramoleculeName: C. elegans TMC-2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Caenorhabditis elegans (invertebrata)

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Macromolecule #1: Transmembrane channel-like protein 2

MacromoleculeName: Transmembrane channel-like protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 136.232609 KDa
Recombinant expressionOrganism: Caenorhabditis elegans (invertebrata)
SequenceString: MPKSGAHQPL VRHDTDDGGE TGQSVKSLAD VSEEEIDSRM SRRSSVIADL LSLFRRSSSV LVRPHTRLGN PNFDDDDDEF DEEDDKEAS KDRILKKIQQ KKEIIQKLRG QPWYMKRKRR TLKVAQKHLQ QQEAKVSKAR LYKAEAGRRL TQASRWLDNL K IYLIPWEA ...String:
MPKSGAHQPL VRHDTDDGGE TGQSVKSLAD VSEEEIDSRM SRRSSVIADL LSLFRRSSSV LVRPHTRLGN PNFDDDDDEF DEEDDKEAS KDRILKKIQQ KKEIIQKLRG QPWYMKRKRR TLKVAQKHLQ QQEAKVSKAR LYKAEAGRRL TQASRWLDNL K IYLIPWEA KIRKIESHFG SVVSSYFTFH RWVLGVNITI TFIMCMFVVI PEWLADSRTQ FGDDRYNKTK AIKVMPPAVR AR ADELSTV WDFGGYFQYS LLFYGFYSKE TFFGETIKYR VPVAYFFCNI FILGFSLFII LRKMAANNRR GTLSSGKTQQ YLF NWKAFT GWDYTIGNPE TAGNVYMANV IKFREAINDD KQKPSDKHPW IRFVARVLTN LFICAMYVFS IWAIMQCGTL KGEH FFAQN ATAITISLIT LVFPNIFDLL GKIEKLHPRN ALRFQLGRVL VLYILNYYTL IYSLMLQLEH LQKEKNASDN PISAL GHPG DAIGRTIRET VLPRYPVDNN PHTYYSYAPV TTTPIPATSS WTTVLPDFGP FGVYNPKASV TKDDTVFSSP VVETHM FGP NSDWNETTVN AASPTGATTR ASLRMSQGGL CWETIIGQEI TKLVTMDLYM TVASIFLIDF LRGLACRYLN LYWPWDL ER TFPEYGEFKV AENVLHLVNN QGMIWLGLFF VPLLPMLNNI KLIILMYIRG WAAMTCNVPA SQIFRASRSS NFFFALLI L FLFLCTLPVG FVIASKTPSK SCGPFGNQSF FYSVITDVLH ENLDKTLVNG IKYSLSPGII IPVLVLLSLV IYFLIAMVT GLSQANQDLS FQLMVERTEE KKKIFELAGG KKKKSKDNTF GKQKPKQLLP PPTKGVSSDD DSQHNRSTAK SVSGRQFVPS LGSVSEVDH STGEEQSSDS ESTTSSLPPK LSLRQRFLVC IGWADPNKYG RHDDIEMEEG GGRLRELSTG SETDSDDEDS E KSNRDMSY RTAIQSFDQN SQSASASSSK STTTAPSNSE MRIEITENPL HTYITPLRIE KKSSASSSSS SHQPSSSIEK QA ARRLLQP ISTTHNIRYG VATVENSSQD PTRPPSTDDS LGDPALHEPL WANLNPHSSY TSAMMSPIMN EVMSNDETTD DEK GRLIPD RPPIPHSPRE LKRLKREKDQ QSESGSKPST PRPPRFRISM SPPRKPPSEK NDSDSSNRKY EMRVEKSPKK PKKS DND

UniProtKB: Transmembrane channel-like protein 2

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Macromolecule #2: CALMyrin (Calcium and Integrin Binding protein) homolog

MacromoleculeName: CALMyrin (Calcium and Integrin Binding protein) homolog
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 23.568568 KDa
Recombinant expressionOrganism: Caenorhabditis elegans (invertebrata)
SequenceString: MGNNASSLSE LNLFSKGGVF TREQLDEYQD CTFFTRKDII RLYKRFYALN PHKVPTNMQG NRPAITTLTF EEVEKMPELK ENPFKRRIC EVFSEDGRGN LSFDDFLDMF SVFSEMAPLQ LKLKYAFRIY DYDGDELLGH DDLSKMIRSL TRDELSDVEV E FIIERIIE ...String:
MGNNASSLSE LNLFSKGGVF TREQLDEYQD CTFFTRKDII RLYKRFYALN PHKVPTNMQG NRPAITTLTF EEVEKMPELK ENPFKRRIC EVFSEDGRGN LSFDDFLDMF SVFSEMAPLQ LKLKYAFRIY DYDGDELLGH DDLSKMIRSL TRDELSDVEV E FIIERIIE EADLDGDSSI NFAEFEHVVS RSPDFIRTFH IRI

UniProtKB: EF-hand domain-containing protein

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Macromolecule #3: Transmembrane inner ear expressed protein

MacromoleculeName: Transmembrane inner ear expressed protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 12.668813 KDa
Recombinant expressionOrganism: Caenorhabditis elegans (invertebrata)
SequenceString:
MPSGNEEINH LSALDQFVAP GLRLWMLIAL VGGVLLIMIV IVCCFMRIRI PRTKRQIDLI AAKRKLRKST KNSAEANAHN DERAQAIVM NSMPSGGGGG APSTSSSRHT GSRIQSQV

UniProtKB: Transmembrane inner ear

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Macromolecule #6: DOCOSANE

MacromoleculeName: DOCOSANE / type: ligand / ID: 6 / Number of copies: 6 / Formula: TWT
Molecular weightTheoretical: 310.601 Da
Chemical component information

ChemComp-TWT:
DOCOSANE

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Macromolecule #7: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

MacromoleculeName: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 7 / Number of copies: 10 / Formula: PEE
Molecular weightTheoretical: 744.034 Da
Chemical component information

ChemComp-PEE:
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE, phospholipid*YM

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Macromolecule #8: HEXADECANE

MacromoleculeName: HEXADECANE / type: ligand / ID: 8 / Number of copies: 22 / Formula: R16
Molecular weightTheoretical: 226.441 Da
Chemical component information

ChemComp-R16:
HEXADECANE

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Macromolecule #9: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 9 / Number of copies: 2 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #10: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 10 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #11: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 11 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #12: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 12 / Number of copies: 4 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statetissue

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Sample preparation

Concentration0.003 mg/mL
BufferpH: 8 / Details: 50 mM Tris pH 8.0, 150 mM NaCl, 0.02% GDN
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV
DetailsNative TMC-2 complex, isolated from transgenic C. elegans.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7usw

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 207726
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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