[English] 日本語
Yorodumi
- EMDB-26741: Structure of Expanded C. elegans TMC-1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-26741
TitleStructure of Expanded C. elegans TMC-1 complex
Map data
Sample
  • Complex: Native TMC-1 complex
    • Protein or peptide: x 3 types
  • Ligand: x 9 types
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 / monoatomic ion channel activity / calcium ion homeostasis / monoatomic ion transmembrane transport / neuronal cell body ...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 / monoatomic ion channel activity / calcium ion homeostasis / monoatomic ion transmembrane transport / 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
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: 3.1 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_26741.png

Downloads & links

-
Map

FileDownload / File: emd_26741.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.84 Å/pix.
x 400 pix.
= 335.6 Å		0.84 Å/pix.
x 400 pix.
= 335.6 Å		0.84 Å/pix.
x 400 pix.
= 335.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.839 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.0
Minimum - Maximum-38.103535000000001 - 59.46566
Average (Standard dev.)0.000000000000906 (±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

-
Half map: #2

Fileemd_26741_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_26741_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
  • Ligand: CALCIUM ION
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: undecan-1-ol
  • Ligand: DODECANE
  • Ligand: CHOLESTEROL
  • Ligand: HEXADECANE
  • 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-#3
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 430 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: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 8 / Formula: CA
Molecular weightTheoretical: 40.078 Da

+
Macromolecule #5: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

MacromoleculeName: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 5 / 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

+
Macromolecule #6: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 6 / Number of copies: 2 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

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

+
Macromolecule #7: undecan-1-ol

MacromoleculeName: undecan-1-ol / type: ligand / ID: 7 / Number of copies: 34 / Formula: ZFC
Molecular weightTheoretical: 172.308 Da
Chemical component information

ChemComp-ZFC:
undecan-1-ol

+
Macromolecule #8: DODECANE

MacromoleculeName: DODECANE / type: ligand / ID: 8 / Number of copies: 12 / Formula: D12
Molecular weightTheoretical: 170.335 Da
Chemical component information

ChemComp-D12:
DODECANE

+
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

+
Macromolecule #10: HEXADECANE

MacromoleculeName: HEXADECANE / type: ligand / ID: 10 / Number of copies: 4 / Formula: R16
Molecular weightTheoretical: 226.441 Da
Chemical component information

ChemComp-R16:
HEXADECANE

+
Macromolecule #11: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 11 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

+
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #0 - Average electron dose: 50.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #1 - 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 / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing #1

Image processing ID1
Image recording ID1
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 142396
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
Image processing #2

Image processing ID2
Image recording ID1
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 142396
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
Image processing #3

Image processing ID3
Image recording ID1
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 142396
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
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