2AGJ

Crystal Structure of a glycosylated Fab from an IgM cryoglobulin with properties of a natural proteolytic antibody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of a glycosylated Fab from an IgM cryoglobulin with properties of a natural proteolytic antibody

Ramsland, P.A.Terzyan, S.S.Cloud, G.Bourne, C.R.Farrugia, W.Tribbick, G.Geysen, H.M.Moomaw, C.R.Slaughter, C.A.Edmundson, A.B.

(2006) Biochem.J. 395: 473-481

  • DOI: 10.1042/BJ20051739

  • PubMed Abstract: 
  • The 2.6 A (1 A=0.1 nm) resolution structure has been determined for the glycosylated Fab (fragment antigen binding) of an IgM (Yvo) obtained from a subject with Waldenström's macroglobulinaemia. Dynamic light scattering was used to estimate the gel p ...

    The 2.6 A (1 A=0.1 nm) resolution structure has been determined for the glycosylated Fab (fragment antigen binding) of an IgM (Yvo) obtained from a subject with Waldenström's macroglobulinaemia. Dynamic light scattering was used to estimate the gel point and monitor the formation of an ordered hydroscopic gel of Yvo IgM upon cooling. If a cryoglobulin forms gels in peripheral tissues and organs, the associated swelling and damage to microvasculature can result in considerable morbidity and mortality. The three-dimensional structure of the branched N-linked oligosaccharide associated with the CH1 domain (first constant domain of heavy chain) is reported. The carbohydrate may act to shield part of the lateral surface of the CH1 domain and crowd the junction between the CH1 and CH2 domains, thereby limiting the segmental flexibility of the Fab arms in intact Yvo IgM, especially at low temperatures. Recently, Yvo IgM was shown to have the properties of a naturally occurring proteolytic antibody [Paul, Karle, Planque, Taguchi, Salas, Nishiyama, Handy, Hunter, Edmundson and Hanson (2004) J. Biol. Chem. 279, 39611-39619; Planque, Bangale, Song, Karle, Taguchi, Poindexter, Bick, Edmundson, Nishiyama and Paul (2004) J. Biol Chem. 279, 14024-14032]. The Yvo protein displayed the ability to cleave, by a nucleophilic mechanism, the amide bonds of a variety of serine protease substrates and the gp120 coat protein of HIV. An atypical serine, arginine and glutamate motif is located in the middle of the Yvo antigen-binding site and displays an overall geometry that mimics the classical serine, histidine and aspartate catalytic triad of serine proteases. Our present findings indicate that pre-existing or natural antibodies can utilize at least one novel strategy for the cleavage of peptide bonds.


    Related Citations: 
    • Interconversion of different crystal forms of Fabs from human IgM cryoglobulins
      Ramsland, P.A.,Upshaw, J.L.,Shultz, B.B.,DeWitt, C.R.,Chissoe III, W.F.,Raison, R.L.,Edmundson, A.B.
      (2001) J.Cryst.Growth 232: 204
    • Dealing with intractable protein cores: protein sequencing of the Mcg IgG and the Yvo IgM heavy chain variable domains
      Shaw, D.C.,Shultz, B.B.,Ramsland, P.A.,Edmundson, A.B.
      (2002) J.Mol.Recog. 15: 341


    Organizational Affiliation

    Structural Immunology Laboratory, Austin Research Institute, Kronheimer Building, Austin Health, Studley Road, Heidelberg, VIC 3084, Australia. p.ramsland@ari.unimelb.edu.au




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Yvo Fab, Light Chain
L
215Homo sapiensGene Names: IGK@
Find proteins for Q6PJF2 (Homo sapiens)
Go to UniProtKB:  Q6PJF2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Yvo Fab, Heavy Chain
H
226Homo sapiensGene Names: IGHM
Find proteins for P01871 (Homo sapiens)
Go to UniProtKB:  P01871
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
H
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
H
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.219 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 82.433α = 90.00
b = 103.653β = 90.00
c = 138.715γ = 90.00
Software Package:
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-05-02
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description