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PDBsum entry 1xed
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protein metals Protein-protein interface(s) links
Immune system PDB id
1xed

 

 

 

 

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Contents
Protein chains
111 a.a. *
105 a.a. *
111 a.a. *
Metals
_MG ×2
Waters ×158
* Residue conservation analysis
PDB id:
1xed
Name: Immune system
Title: Crystal structure of a ligand-binding domain of the human polymeric ig receptor, pigr
Structure: Polymeric-immunoglobulin receptor. Chain: a, b, c, d, e, f. Fragment: n-terminal domain i. Synonym: poly-ig receptor, pigr, ig-like v-type 1 domain. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: pigr. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
Resolution:
1.90Å     R-factor:   0.183     R-free:   0.244
Authors: A.E.Hamburger,A.P.West Jr.,P.J.Bjorkman
Key ref:
A.E.Hamburger et al. (2004). Crystal structure of a polymeric immunoglobulin binding fragment of the human polymeric immunoglobulin receptor. Structure, 12, 1925-1935. PubMed id: 15530357 DOI: 10.1016/j.str.2004.09.006
Date:
10-Sep-04     Release date:   23-Nov-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P01833  (PIGR_HUMAN) -  Polymeric immunoglobulin receptor from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		764 a.a.
111 a.a.*
Protein chains
Pfam   ArchSchema ?
P01833  (PIGR_HUMAN) -  Polymeric immunoglobulin receptor from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		764 a.a.
105 a.a.*
Protein chains
Pfam   ArchSchema ?
P01833  (PIGR_HUMAN) -  Polymeric immunoglobulin receptor from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		764 a.a.
111 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 14 residue positions (black crosses)

 

 
DOI no: 10.1016/j.str.2004.09.006 Structure 12:1925-1935 (2004)
PubMed id: 15530357  
 
 
Crystal structure of a polymeric immunoglobulin binding fragment of the human polymeric immunoglobulin receptor.
A.E.Hamburger, A.P.West, P.J.Bjorkman.
 
  ABSTRACT  
 
The polymeric immunoglobulin receptor (pIgR) is a type I transmembrane protein that delivers dimeric IgA (dIgA) and pentameric IgM to mucosal secretions. Here, we report the 1.9 A resolution X-ray crystal structure of the N-terminal domain of human pIgR, which binds dIgA in the absence of other pIgR domains with an equilibrium dissociation constant of 300 nM. The structure of pIgR domain 1 reveals a folding topology similar to immunoglobulin variable domains, but with differences in the counterparts of the complementarity determining regions (CDRs), including a helical turn in CDR1 and a CDR3 loop that points away from the other CDRs. The unusual CDR3 loop position prevents dimerization analogous to the pairing of antibody variable heavy and variable light domains. The pIgR domain 1 structure allows interpretation of previous mutagenesis results and structure-based comparisons between pIgR and other IgA receptors.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Mutagenesis Data Mapped onto StructureThe positions of substitutions that abolished (red) or decreased (blue) pIgA binding to rabbit pIgR (Coyne et al., 1994) are mapped onto the human pIgR D1 structure. A close-up of the CDR1 region is shown in the upper right, and the sequence of CDR1 in human and rabbit pIgR D1 is shown in the lower right. Val29 (black), which is solvent exposed in the D1 structure, was assumed to be buried and was therefore not substituted (Bakos et al. 1993 and Coyne et al. 1994).
 
  The above figure is reprinted by permission from Cell Press: Structure (2004, 12, 1925-1935) copyright 2004.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20083120 F.Faucher, S.S.Wallace, and S.Doublié (2010).
The C-terminal lysine of Ogg2 DNA glycosylases is a major molecular determinant for guanine/8-oxoguanine distinction.
  J Mol Biol, 397, 46-56.
PDB code: 3knt
19079336 A.Bonner, A.Almogren, P.B.Furtado, M.A.Kerr, and S.J.Perkins (2009).
Location of secretory component on the Fc edge of dimeric IgA1 reveals insight into the role of secretory IgA1 in mucosal immunity.
  Mucosal Immunol, 2, 74-84.
PDB code: 3chn
19307722 D.Hamdane, C.Lechauve, M.C.Marden, and B.Golinelli-Pimpaneau (2009).
Pseudo-merohedral twinning in monoclinic crystals of wild-type human brain neuroglobin.
  Acta Crystallogr D Biol Crystallogr, 65, 388-392.  
19858324 H.Kubagawa, S.Oka, Y.Kubagawa, I.Torii, E.Takayama, D.W.Kang, G.L.Gartland, L.F.Bertoli, H.Mori, H.Takatsu, T.Kitamura, H.Ohno, and J.Y.Wang (2009).
Identity of the elusive IgM Fc receptor (FcmuR) in humans.
  J Exp Med, 206, 2779-2793.  
18214466 C.Neylon (2008).
Small angle neutron and X-ray scattering in structural biology: recent examples from the literature.
  Eur Biophys J, 37, 531-541.  
17428798 A.Bonner, C.Perrier, B.Corthésy, and S.J.Perkins (2007).
Solution structure of human secretory component and implications for biological function.
  J Biol Chem, 282, 16969-16980.
PDB code: 2ocw
  19662225 J.M.Kneller, T.Ehlen, J.P.Matisic, D.Miller, D.Van Niekerk, W.L.Lam, M.Marra, R.Richards-Kortum, M.Follen, C.Macaulay, and S.J.Jones (2007).
Using LongSAGE to Detect Biomarkers of Cervical Cancer Potentially Amenable to Optical Contrast Agent Labelling.
  Biomark Insights, 2, 447-461.  
17573702 T.N.Kazeeva, and A.B.Shevelev (2007).
Unknown functions of immunoglobulins A.
  Biochemistry (Mosc), 72, 485-494.  
16866880 B.D.Wines, and P.M.Hogarth (2006).
IgA receptors in health and disease.
  Tissue Antigens, 68, 103-114.  
16543244 C.Perrier, N.Sprenger, and B.Corthésy (2006).
Glycans on secretory component participate in innate protection against mucosal pathogens.
  J Biol Chem, 281, 14280-14287.  
16646632 E.R.Sprague, C.Wang, D.Baker, and P.J.Bjorkman (2006).
Crystal structure of the HSV-1 Fc receptor bound to Fc reveals a mechanism for antibody bipolar bridging.
  PLoS Biol, 4, e148.
PDB codes: 2giy 2gj7
16362985 J.M.Woof, and M.A.Kerr (2006).
The function of immunoglobulin A in immunity.
  J Pathol, 208, 270-282.  
16738934 J.P.Cannon, R.N.Haire, M.G.Mueller, R.T.Litman, D.D.Eason, D.Tinnemore, C.T.Amemiya, T.Ota, and G.W.Litman (2006).
Ancient divergence of a complex family of immune-type receptor genes.
  Immunogenetics, 58, 362-373.  
17043868 M.M.Gomes, and A.B.Herr (2006).
IgA and IgA-specific receptors in human disease: structural and functional insights into pathogenesis and therapeutic potential.
  Springer Semin Immunopathol, 28, 383-395.  
16790931 R.C.Hillig, and L.Renault (2006).
Detecting and overcoming hemihedral twinning during the MIR structure determination of Rna1p.
  Acta Crystallogr D Biol Crystallogr, 62, 750-765.
PDB code: 2ca6
16048543 C.S.Kaetzel (2005).
The polymeric immunoglobulin receptor: bridging innate and adaptive immune responses at mucosal surfaces.
  Immunol Rev, 206, 83-99.  
16048542 J.M.Woof, and J.Mestecky (2005).
Mucosal immunoglobulins.
  Immunol Rev, 206, 64-82.  
15735347 L.Lehtiö, I.Fabrichniy, T.Hansen, P.Schönheit, and A.Goldman (2005).
Unusual twinning in an acetyl coenzyme A synthetase (ADP-forming) from Pyrococcus furiosus.
  Acta Crystallogr D Biol Crystallogr, 61, 350-354.  
16252250 R.L.Rich, and D.G.Myszka (2005).
Survey of the year 2004 commercial optical biosensor literature.
  J Mol Recognit, 18, 431-478.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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