5D4K | pdb_00005d4k

Crystal structure of the human polymeric Ig receptor (pIgR) ectodomain

• PDB DOI: https://doi.org/10.2210/pdb5D4K/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2015-08-07 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: 2.60 Å
• R-Value Free: 
  0.254 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.201 (Depositor) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

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 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.
Jules Stein Eye Institute, University of California, Los Angeles, United States.
Department of Chemistry and Biochemistry, University of California, Los Angeles, United States.

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: 125.41 kDa 
• Atom Count: 8,530 
• Modeled Residue Count: 1,075 
• Deposited Residue Count: 1,114 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polymeric immunoglobulin receptor	A, B	557	Homo sapiens	Mutation(s): 1  Gene Names: PIGR
UniProt & NIH Common Fund Data Resources
Find proteins for P01833 (Homo sapiens) Explore P01833  Go to UniProtKB:  P01833
PHAROS:  P01833 GTEx:  ENSG00000162896
Glycosylation
Glycosylation Sites: 4		Go to GlyGen: P01833-1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], F [auth A], G [auth A], J [auth B], K [auth B], L [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	H [auth A], I [auth A], M [auth B], N [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.254 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.201 (Depositor) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.258	α = 90
b = 242.434	β = 114.89
c = 63.046	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
Coot	model building
Blu-Ice	data collection
XDS	data reduction

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

Revision History  

• Version 1.0: 2016-03-16
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence, Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.2: 2024-11-13
  Changes: Structure summary