8TKP | pdb_00008tkp

Structure of the C. elegans TMC-2 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: TISSUE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8TKP

This is version 1.0 of the entry. See complete history

Literature

The structure of the Caenorhabditis elegans TMC-2 complex suggests roles of lipid-mediated subunit contacts in mechanosensory transduction.

Clark, S.Jeong, H.Posert, R.Goehring, A.Gouaux, E.

(2024) Proc Natl Acad Sci U S A 121: e2314096121-e2314096121

  • DOI: https://doi.org/10.1073/pnas.2314096121
  • Primary Citation Related Structures: 
    8TKP

  • PubMed 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 of membrane proteins whose function has been linked to a variety of mechanosensory processes, including hearing and balance sensation in vertebrates and locomotion in Drosophila . TMC1 and TMC2 are components of ion channel complexes, but the molecular features that tune these complexes to diverse mechanical stimuli are unknown. Caenorhabditis elegans 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 C. elegans . 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 C. elegans 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.


  • Organizational Affiliation
    • Vollum Institute, Oregon Health and Science University, Portland, OR 97239.

Macromolecule Content 

  • Total Structure Weight: 362.48 kDa 
  • Atom Count: 14,666 
  • Modeled Residue Count: 1,698 
  • Deposited Residue Count: 3,042 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transmembrane channel-like protein 2
A, D
1,203Caenorhabditis elegansMutation(s): 0 
Gene Names: tmc-2B0416.1
Membrane Entity: Yes 
UniProt
Find proteins for Q11069 (Caenorhabditis elegans)
Explore Q11069 
Go to UniProtKB:  Q11069
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ11069
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
CALMyrin (Calcium and Integrin Binding protein) homolog
B, E
201Caenorhabditis elegansMutation(s): 0 
Gene Names: calm-1CELE_F30A10.1F30A10.1
UniProt
Find proteins for Q93640 (Caenorhabditis elegans)
Explore Q93640 
Go to UniProtKB:  Q93640
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93640
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Transmembrane inner ear expressed protein
C, F
117Caenorhabditis elegansMutation(s): 0 
Gene Names: CELE_Y39A1C.1Y39A1C.1
Membrane Entity: Yes 
UniProt
Find proteins for Q9XXE7 (Caenorhabditis elegans)
Explore Q9XXE7 
Go to UniProtKB:  Q9XXE7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9XXE7
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth H]2N-Glycosylation
Glycosylation Resources
GlyTouCan: G79924RM
GlyCosmos: G79924RM
GlyGen: G79924RM
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseH [auth G]2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEE

Query on PEE



Download:Ideal Coordinates CCD File
FA [auth C]
IA [auth D]
J [auth A]
RA [auth D]
S [auth A]
FA [auth C],
IA [auth D],
J [auth A],
RA [auth D],
S [auth A],
SA [auth D],
T [auth A],
UA [auth D],
V [auth A],
XA [auth D]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
CLR

Query on CLR



Download:Ideal Coordinates CCD File
LA [auth D],
M [auth A]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
TWT

Query on TWT



Download:Ideal Coordinates CCD File
BA [auth C]
BB [auth F]
HA [auth D]
I [auth A]
VA [auth D]
BA [auth C],
BB [auth F],
HA [auth D],
I [auth A],
VA [auth D],
W [auth A]
DOCOSANE
C22 H46
HOWGUJZVBDQJKV-UHFFFAOYSA-N
PLM
(Subject of Investigation/LOI)

Query on PLM



Download:Ideal Coordinates CCD File
EA [auth C],
EB [auth F],
FB [auth F],
GA [auth C]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
R16

Query on R16



Download:Ideal Coordinates CCD File
CA [auth C]
CB [auth F]
DA [auth C]
DB [auth F]
JA [auth D]
CA [auth C],
CB [auth F],
DA [auth C],
DB [auth F],
JA [auth D],
K [auth A],
KA [auth D],
L [auth A],
MA [auth D],
N [auth A],
NA [auth D],
O [auth A],
OA [auth D],
P [auth A],
PA [auth D],
Q [auth A],
QA [auth D],
R [auth A],
TA [auth D],
U [auth A],
Y [auth A],
YA [auth D]
HEXADECANE
C16 H34
DCAYPVUWAIABOU-UHFFFAOYSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
WA [auth D],
X [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
AA [auth B],
AB [auth E],
Z [auth B],
ZA [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: TISSUE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-27
    Type: Initial release