5T4M

Crystal Structure of Human Protocadherin-15 EC3-5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A Partial Calcium-Free Linker Confers Flexibility to Inner-Ear Protocadherin-15.

Powers, R.E.Gaudet, R.Sotomayor, M.

(2017) Structure 25: 482-495

  • DOI: 10.1016/j.str.2017.01.014
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Tip links of the inner ear are protein filaments essential for hearing and balance. Two atypical cadherins, cadherin-23 and protocadherin-15, interact in a Ca <sup>2+ </sup>-dependent manner to form tip links. The largely unknown structure and mechan ...

    Tip links of the inner ear are protein filaments essential for hearing and balance. Two atypical cadherins, cadherin-23 and protocadherin-15, interact in a Ca 2+ -dependent manner to form tip links. The largely unknown structure and mechanics of these proteins are integral to understanding how tip links pull on ion channels to initiate sensory perception. Protocadherin-15 has 11 extracellular cadherin (EC) repeats. Its EC3-4 linker lacks several of the canonical Ca 2+ -binding residues, and contains an aspartate-to-alanine polymorphism (D414A) under positive selection in East Asian populations. We present structures of protocadherin-15 EC3-5 featuring two Ca 2+ -binding linker regions: canonical EC4-5 linker binding three Ca 2+ ions, and non-canonical EC3-4 linker binding only two Ca 2+ ions. Our structures and biochemical assays reveal little difference between the D414 and D414A variants. Simulations predict that the partial Ca 2+ -free EC3-4 linker exhibits increased flexural flexibility without compromised mechanical strength, providing insight into the dynamics of tip links and other atypical cadherins.


    Organizational Affiliation

    Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA. Electronic address: gaudet@mcb.harvard.edu.,Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12(th) Avenue, Columbus, OH 43210, USA. Electronic address: sotomayor.8@osu.edu.,Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA; Biophysics Graduate Program, Harvard University, Boston, MA 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protocadherin-15
A, B
365Homo sapiensMutation(s): 0 
Gene Names: PCDH15 (USH1F)
Find proteins for Q96QU1 (Homo sapiens)
Go to Gene View: PCDH15
Go to UniProtKB:  Q96QU1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.189 
  • Space Group: P 65
  • Diffraction Data DOI: 
    10.15785/SBGRID/361 SBGrid
Unit Cell:
Length (Å)Angle (°)
a = 105.608α = 90.00
b = 105.608β = 90.00
c = 193.672γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
Cootmodel building
HKL-2000data collection
PHENIXphasing
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)United StatesK99/R00 DC012534
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)United StatesR01 DC02281

Revision History 

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence
  • Version 1.2: 2018-08-01
    Type: Data collection, Database references
  • Version 1.3: 2019-12-18
    Type: Author supporting evidence