3L9B

Crystal Structure of Rat Otoferlin C2A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of the C2A domain of otoferlin reveals an unconventional top loop region.

Helfmann, S.Neumann, P.Tittmann, K.Moser, T.Ficner, R.Reisinger, E.

(2011) J.Mol.Biol. 406: 479-490

  • DOI: 10.1016/j.jmb.2010.12.031

  • PubMed Abstract: 
  • Otoferlin (Otof), whose genetic mutations cause profound deafness in humans, is a protein composed of at least six C(2) domains, which are known as Ca(2)(+)-binding and phospholipid-binding regions. Mammalian ferlin proteins are proposed to act in me ...

    Otoferlin (Otof), whose genetic mutations cause profound deafness in humans, is a protein composed of at least six C(2) domains, which are known as Ca(2)(+)-binding and phospholipid-binding regions. Mammalian ferlin proteins are proposed to act in membrane fusion events, with Otof being specifically required for exocytosis in auditory hair cells. Ferlin C(2) domains exhibit a rather low level of sequence similarity to those of synaptotagmins, protein kinase C isoforms, or phospholipases. Here, we report the crystal structure of the N-terminal C(2) domain of Otof (C₂A) at 1.95-Å resolution. In contrast to previous predictions, we found that this C(2) domain is complete with eight β-strands. Comparing the structure of Otof C₂A to those of other C(2) domains revealed one top loop in Otof to be significantly shorter. This results in a depression of the surface, which is positively charged for the Otof C₂A domain, and contrasts with the head-like protrusion surrounded by a negatively charged "neck" typically found in other C(2) domains. Isothermal titration calorimetry and circular dichroism spectroscopy studies confirmed that Otof C₂A is unable to bind Ca(2+), while the synaptotagmin-1 C₂A domain exhibited Ca(2+) binding under the same conditions. Furthermore, floatation assays revealed a failure of Otof C(2)A to bind to phospholipid membranes. Accordingly, no positively charged β-groove-like surface structure, which is known to bind phosphatidylinositol-4,5-bisphosphate in other C(2) domains, was found at the respective position in Otof C₂A. Taken together, these data demonstrate that the Otof C₂A domain differs structurally and functionally from other C(2) domains.


    Organizational Affiliation

    Molecular Biology of Cochlear Neurotransmission Junior Research Group, University Medical Center Göttingen, Robert-Koch-Str. 40, 37099 Göttingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Otoferlin
A
144Rattus norvegicusMutation(s): 0 
Gene Names: Otof (Fer1l2)
Find proteins for Q9ERC5 (Rattus norvegicus)
Go to UniProtKB:  Q9ERC5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.181 
  • Space Group: I 41
Unit Cell:
Length (Å)Angle (°)
a = 100.300α = 90.00
b = 100.300β = 90.00
c = 30.000γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction
PHENIXrefinement
XSCALEdata scaling
MAR345dtbdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-09-17
    Type: Database references