5F1S

Crystal structure of the teleost fish polymeric Ig receptor (pIgR) ectodomain

• PDB DOI: https://doi.org/10.2210/pdb5F1S/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Oncorhynchus mykiss
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2015-11-30 Released: 2016-03-16 
• Deposition Author(s): Stadtmueller, B.M., Bjorkman, P.J.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Cancer Research Institute

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.215 
• R-Value Work: 0.185 
• R-Value Observed: 0.188 

Literature

The structure and dynamics of secretory component and its interactions with polymeric immunoglobulins.

Stadtmueller, B.M., Huey-Tubman, K.E., Lopez, C.J., Yang, Z., Hubbell, W.L., Bjorkman, P.J.

(2016) Elife 5

• PubMed: 26943617 
• DOI: https://doi.org/10.7554/eLife.10640
• Primary Citation of Related Structures:  
  5D4K, 5F1S


• PubMed Abstract: 
  

  As a first-line vertebrate immune defense, the polymeric immunoglobulin receptor (pIgR) transports polymeric IgA and IgM across epithelia to mucosal secretions, where the cleaved ectodomain (secretory component; SC) becomes a component of secretory antibodies, or when unliganded, binds and excludes bacteria. Here we report the 2.6Å crystal structure of unliganded human SC (hSC) and comparisons with a 1.7Å structure of teleost fish SC (tSC), an early pIgR ancestor. The hSC structure comprises five immunoglobulin-like domains (D1-D5) arranged as a triangle, with an interface between ligand-binding domains D1 and D5. Electron paramagnetic resonance measurements confirmed the D1-D5 interface in solution and revealed that it breaks upon ligand binding. Together with binding studies of mutant and chimeric SCs, which revealed domain contributions to secretory antibody formation, these results provide detailed models for SC structure, address pIgR evolution, and demonstrate that SC uses multiple conformations to protect mammals from pathogens.

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Organizational Affiliation: 

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 24.39 kDa 
• Atom Count: 1,745 
• Modelled Residue Count: 206 
• Deposited Residue Count: 219 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
polymeric Immunoglobulin Receptor	A	219	Oncorhynchus mykiss	Mutation(s): 0
UniProt
Find proteins for A0A060Y6X8 (Oncorhynchus mykiss) Explore A0A060Y6X8  Go to UniProtKB:  A0A060Y6X8

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.215 
• R-Value Work: 0.185 
• R-Value Observed: 0.188 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.938	α = 90
b = 54.938	β = 90
c = 187.257	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
SHELXDE	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-03-16 
Deposition Author(s): Stadtmueller, B.M., Bjorkman, P.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI04123
Cancer Research Institute	United States	Irving Postdoctoral Fellowship to B. Stadtmueller

Revision History  

• Version 1.0: 2016-03-16
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence, Derived calculations, Refinement description
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence