5D4K

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.254
R-Value Work: 0.201
R-Value Observed: 0.203

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 125.41 kDa
Atom Count: 8,530
Modelled Residue Count: 1,075
Deposited Residue Count: 1,114
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01833
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	2		N-Glycosylation	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B]	E [auth A] F [auth A] G [auth A] J [auth B] K [auth B] 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		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B]	H [auth A], I [auth A], M [auth B], N [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.254
R-Value Work: 0.201
R-Value Observed: 0.203
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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-03-16

Deposition Author(s):

Stadtmueller, B.M.

Bjorkman, P.J.

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 (Full details and data files)

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