5K8R

Structure of human clustered protocadherin gamma B3 EC1-4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Antiparallel protocadherin homodimers use distinct affinity- and specificity-mediating regions in cadherin repeats 1-4.

Nicoludis, J.M.Vogt, B.E.Green, A.G.Scharfe, C.P.Marks, D.S.Gaudet, R.

(2016) Elife 5: --

  • DOI: 10.7554/eLife.18449

  • PubMed Abstract: 
  • Protocadherins (Pcdhs) are cell adhesion and signaling proteins used by neurons to develop and maintain neuronal networks, relying on trans homophilic interactions between their extracellular cadherin (EC) repeat domains. We present the structure of ...

    Protocadherins (Pcdhs) are cell adhesion and signaling proteins used by neurons to develop and maintain neuronal networks, relying on trans homophilic interactions between their extracellular cadherin (EC) repeat domains. We present the structure of the antiparallel EC1-4 homodimer of human PcdhγB3, a member of the γ subfamily of clustered Pcdhs. Structure and sequence comparisons of α, β, and γ clustered Pcdh isoforms illustrate that subfamilies encode specificity in distinct ways through diversification of loop region structure and composition in EC2 and EC3, which contains isoform-specific conservation of primarily polar residues. In contrast, the EC1/EC4 interface comprises hydrophobic interactions that provide non-selective dimerization affinity. Using sequence coevolution analysis, we found evidence for a similar antiparallel EC1-4 interaction in non-clustered Pcdh families. We thus deduce that the EC1-4 antiparallel homodimer is a general interaction strategy that evolved before the divergence of these distinct protocadherin families.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States.,Department of Systems Biology, Harvard Medical School, Boston, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States.,Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protocadherin gamma-B3
A
414Homo sapiensMutation(s): 0 
Gene Names: PCDHGB3
Find proteins for Q9Y5G1 (Homo sapiens)
Go to UniProtKB:  Q9Y5G1
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 128.881α = 90.00
b = 161.229β = 90.00
c = 53.659γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling
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 of General Medical Sciences (NIH/NIGMS)United StatesP41 GM103403

Revision History 

  • Version 1.0: 2016-08-24
    Type: Initial release
  • Version 1.1: 2017-09-13
    Type: Author supporting evidence, Derived calculations
  • Version 1.2: 2019-12-25
    Type: Author supporting evidence