8Z3F | pdb_00008z3f

Complex structure of CIB2 and TMC1 CR1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 
    0.200 (Depositor), 0.201 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Mechano-electrical transduction components TMC1-CIB2 undergo a Ca 2+ -induced conformational change linked to hearing loss.

Wu, S.Lin, L.Hu, Q.Yao, X.Wang, H.Liu, S.Liu, Q.Xi, Y.Lin, Y.Gong, J.Hu, R.Zhan, W.Luo, Y.He, G.Liu, Z.Xiong, W.Wang, Q.Xu, Z.Bai, F.Lu, Q.

(2025) Dev Cell 60: 1586

  • DOI: https://doi.org/10.1016/j.devcel.2025.01.004
  • Primary Citation of Related Structures:  
    8Z3F

  • PubMed Abstract: 

    TMC1, a unique causative gene associated with deafness, exhibits variants with autosomal dominant and recessive inheritance patterns. TMC1 codes for the transmembrane channel-like protein 1 (TMC1), a key component of the mechano-electrical transduction (MET) machinery for hearing. However, the molecular mechanism of Ca 2+ regulation in MET remains unclear. Calcium and integrin-binding protein 2 (CIB2), another MET component associated with deafness, can bind with Ca 2+ . Our study shows that TMC1-CIB2 complex undergoes a Ca 2+ -induced conformational change. We identified a vertebrate-specific binding site on TMC1 that interacts with apo CIB2, linked with hearing loss. Using an ex vivo mouse organotypic cochlea model, we demonstrated that disruption of the calcium-binding site of CIB2 perturbs the MET channel conductivity. After systematically analyzing the hearing loss variants, we observed dominant mutations of TMC1 cluster around the putative ion pore or at the binding interfaces with CIB2. These findings elucidate the molecular mechanisms underlying TMC1-linked hearing loss.


  • Organizational Affiliation
    • Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200030, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Calcium and integrin-binding family member 2191Mus musculusMutation(s): 1 
Gene Names: Cib2Kip2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Z309 (Mus musculus)
Explore Q9Z309 
Go to UniProtKB:  Q9Z309
IMPC:  MGI:1929293
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Z309
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane channel-like protein 154Mus musculusMutation(s): 0 
Gene Names: Tmc1Bthdn
UniProt & NIH Common Fund Data Resources
Find proteins for Q8R4P5 (Mus musculus)
Explore Q8R4P5 
Go to UniProtKB:  Q8R4P5
IMPC:  MGI:2151016
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8R4P5
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free:  0.200 (Depositor), 0.201 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.177α = 90
b = 36.225β = 98.869
c = 63.496γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-19
    Type: Initial release
  • Version 1.1: 2025-06-25
    Changes: Database references