5T4M | pdb_00005t4m

Crystal Structure of Human Protocadherin-15 EC3-5

• PDB DOI: https://doi.org/10.2210/pdb5T4M/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-08-29 Released: 2017-02-22 
• Deposition Author(s): Powers, R.E., Gaudet, R., Sotomayor, M.
• Funding Organization(s): National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 
  0.221 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.195 (DCC) 

Starting Model: experimental

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

• PubMed: 28238533 
• DOI: https://doi.org/10.1016/j.str.2017.01.014
• Primary Citation Related Structures: 
  5T4M, 5T4N


• 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 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.

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Organizational Affiliation: 
• Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA; Biophysics Graduate Program, Harvard University, Boston, MA 02115, USA.
Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA. Electronic address: [e-mail].
Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12(th) Avenue, Columbus, OH 43210, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 82.2 kDa 
• Atom Count: 5,725 
• Modeled Residue Count: 693 
• Deposited Residue Count: 730 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protocadherin-15	A, B	365	Homo sapiens	Mutation(s): 0  Gene Names: PCDH15, USH1F
UniProt & NIH Common Fund Data Resources
Find proteins for Q96QU1 (Homo sapiens) Explore Q96QU1  Go to UniProtKB:  Q96QU1
PHAROS:  Q96QU1 GTEx:  ENSG00000150275

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free:  0.221 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.195 (DCC) 

Diffraction Data: https://doi.org/10.15785/SBGRID/361

Diffraction Data: https://doi.org/10.15785/SBGRID/362

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.608	α = 90
b = 105.608	β = 90
c = 193.672	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data collection
HKL-2000	data scaling
Coot	model building
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-02-22 
Deposition Author(s): Powers, R.E., Gaudet, R., Sotomayor, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)	United States	K99/R00 DC012534
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)	United States	R01 DC02281

Revision History  

• Version 1.0: 2017-02-22
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence
• Version 1.2: 2018-08-01
  Changes: Data collection, Database references
• Version 1.3: 2019-12-18
  Changes: Author supporting evidence
• Version 1.4: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-10-23
  Changes: Structure summary