[English] 日本語
Yorodumi
- EMDB-26743: Structure of C. elegans TMC-1 complex with ARRD-6 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-26743
TitleStructure of C. elegans TMC-1 complex with ARRD-6
Map dataVolume
Sample
  • Complex: Native TMC-1 complex
    • Protein or peptide: Transmembrane channel-like protein 1
    • Protein or peptide: CALMyrin (Calcium and Integrin Binding protein) homolog
    • Protein or peptide: Transmembrane inner ear expressed protein
    • Protein or peptide: ARRestin Domain protein
  • Ligand: CALCIUM IONCalcium
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: PALMITIC ACID
KeywordsComplex / MEMBRANE PROTEIN
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
ARRestin Domain protein / Transmembrane channel-like protein 1 / EF-hand domain-containing protein / Transmembrane inner ear
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.54 Å
AuthorsJeong H / Clark S / Gouaux E
Funding support United States, 1 items
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, 2022-
Header (metadata) releaseOct 19, 2022-
Map releaseOct 19, 2022-
UpdateAug 9, 2023-
Current statusAug 9, 2023Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_26743.png

Downloads & links

-
Map

FileDownload / File: emd_26743.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVolume
Voxel sizeX=Y=Z: 0.839 Å
Density
Contour LevelBy AUTHOR: 6.0
Minimum - Maximum-42.398449999999997 - 66.936620000000005
Average (Standard dev.)-0.000000000002247 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 335.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Additional-Volume

Fileemd_26743_additional_1.map
AnnotationAdditional-Volume
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_26743_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_26743_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Native TMC-1 complex

EntireName: Native TMC-1 complex
Components
  • Complex: Native TMC-1 complex
    • Protein or peptide: Transmembrane channel-like protein 1
    • Protein or peptide: CALMyrin (Calcium and Integrin Binding protein) homolog
    • Protein or peptide: Transmembrane inner ear expressed protein
    • Protein or peptide: ARRestin Domain protein
  • Ligand: CALCIUM IONCalcium
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: PALMITIC ACID

+
Supramolecule #1: Native TMC-1 complex

SupramoleculeName: Native TMC-1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 480 KDa

+
Macromolecule #1: Transmembrane channel-like protein 1

MacromoleculeName: Transmembrane channel-like protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 147.331812 KDa
SequenceString: MQEAARRASL RKEHTPTNEK FGDLSKQDSL GERASSKLTL DDELYDILYA FGETDAFINK GDKQRETDED GNPLTRQALL ERIRQKKEV IGKLRCQAWS MTRKRRTLKL AQKYLEQHES KVSRSHLYME EMRKRARLMK RSFSNFKTYL IPWESKIKRI E SHFGSVVS ...String:
MQEAARRASL RKEHTPTNEK FGDLSKQDSL GERASSKLTL DDELYDILYA FGETDAFINK GDKQRETDED GNPLTRQALL ERIRQKKEV IGKLRCQAWS MTRKRRTLKL AQKYLEQHES KVSRSHLYME EMRKRARLMK RSFSNFKTYL IPWESKIKRI E SHFGSVVS SYFTFLRWIV FVNIMITLIA LVFVVLPETL ADSVANEGRF NRTKTRKQIP ANERVHADEL AVVWHYDGYL RY SPLFYGY YSDDPFLGNK IKYALPLAYF MVTLTIFAYS FFAILRKMAA NARMSKLSGS KAEQYIFNWK LFTGWDYTIG NSE TASNTV MAVVIKLRES IADIKKDAHG KFRLLQFSLR VFANIIICAM LGFSIYCIIF AVQKSQVQDD GNLFTKNQVP SVVS TITHV FPMIFDLIGK MENYHPRTAL RAHLGRVLIL YTVNYITLIF ALFEKMTALR DRVNSTSTSS SHRTKRQQGG WNPNM QRPP PYASRAEVRQ MSDFLAANTR RFQTVSQRTT RSVTTPFTVA PQFGPFNVNN PNAVFHNGTH STSFESQILG PKALPI FTP PPRKYPGFTP GNVGQQFGGP DFPRNQVYTK STPLPRVRTK PPWVYTTTHP PLVQNRAMTT TMSKSAKKGN SKNLDDD IL LSNETIQMSE AALRRNHDGH NNDICWETII GQEIVKLVTM DLIFTILSIL VIDLFRGLWI KYCSSWWCWD IETTFPEY G EFKVAENVLH IINNQGMIWL GLFFAPLLPA INNIKLIILM YIRGWAVMTC NVPAREIFRA SRSSNFYLGI LLIWLLLCT LPVGFVIASM SPSRSCGPFA RYQHFYTVVT REIEKRVDQT VLSYIRHIAS PGVVIPIILF LILIIYFLFS LVRGLREANT DLQAQLVHE RTEEKKKIFE LAGGKKNKFE KDRDKKRSND YIPLIEQRRR EPWRQYHEME ADHALASDSS EESDINEDED D ERQPLTAY PLRAIETPPE TLQVTAFHPS LGSLIENREM EDEESASGDQ LPMIHKSVSF QGPSHMQMRQ SISTESCSQI SR SAIQVAT PEEIRALLRP YLEAKYGIPY QHGIKSFPID VHTPPNNTPS RRSSKYNSFV SLYEHTRDDH KNFVASTIKE TDE DPGKSD KKQTSSKDVA PDFMPWPSAD EARALREKMK SKTPLMLTKT TVEEKPKGGK SSESEFRPPV PIHRKYNIQT TEEE NEEEE TDSAPESSKK RFRISVSPTK TIAPASASRA QHKIVSQASS SSSIPHGRQP DPNKKASLVL PPLRAPRVQF DEDDS PRQI D

UniProtKB: Transmembrane channel-like protein 1

+
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
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

+
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
SequenceString:
MPSGNEEINH LSALDQFVAP GLRLWMLIAL VGGVLLIMIV IVCCFMRIRI PRTKRQIDLI AAKRKLRKST KNSAEANAHN DERAQAIVM NSMPSGGGGG APSTSSSRHT GSRIQSQV

UniProtKB: Transmembrane inner ear

+
Macromolecule #4: ARRestin Domain protein

MacromoleculeName: ARRestin Domain protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 53.103715 KDa
SequenceString: MAEEKKETMI STLLEKHYFQ VEEQKSGMDY ISSFDIRLNK DVYYAGETIS GSVLLENTEN IKIRGIRVLL RGKVHATLKV VKSGERRTL KDDQYVLDEK QLLWGKDKSD ESDSVPILAR GVHQFSFNFD LPQSSLPCSL ESRHCTIRYY FKVIIDIPYA S SPQGIKYF ...String:
MAEEKKETMI STLLEKHYFQ VEEQKSGMDY ISSFDIRLNK DVYYAGETIS GSVLLENTEN IKIRGIRVLL RGKVHATLKV VKSGERRTL KDDQYVLDEK QLLWGKDKSD ESDSVPILAR GVHQFSFNFD LPQSSLPCSL ESRHCTIRYY FKVIIDIPYA S SPQGIKYF TIIGPHIDSM EEKYLSPLSA QDRKVNCCWC CQRGALALRI ILERTAYVCG ENIRVRAQIE NRQSTAQSLV IR LVQHVEV FVEKGLLGEN KMMSCVVFEH KSPAIAANSQ GKYDSTLEQP IRLPVVPPTL VGVCRLIQIY YALRVCMEDE KGN ECLHID FPLTVATIPY RIPNAPPPPV DYDFCSNHVE GGKYVSPEFR LGQVYDGEGE EINKEEEIVL YRPVYVKLAD RRIG SPHVS KDFRSGSFTR IADSSLALVT EPNGSRRRSI LVASNPCLAM RDESMDEKLM MTNGCNSEGD PLVA

UniProtKB: ARRestin Domain protein

+
Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 8 / Formula: CA
Molecular weightTheoretical: 40.078 Da

+
Macromolecule #6: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

MacromoleculeName: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 6 / Number of copies: 2 / Formula: PEE
Molecular weightTheoretical: 744.034 Da
Chemical component information

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

+
Macromolecule #7: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 7 / Number of copies: 2 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM / Phosphatidylethanolamine

+
Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

+
Macromolecule #9: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 9 / Number of copies: 4 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID / Palmitic acid

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing #1

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 99248
Image processing ID1

-
Image processing #2

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 99248
Image processing ID2

+
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