1QLR

CRYSTAL STRUCTURE OF THE FAB FRAGMENT OF A HUMAN MONOCLONAL IgM COLD AGGLUTININ


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Three-Dimensional Structure of the Fab Fragment from a Human Igm Cold Agglutinin

Cauerhff, A.Braden, B.C.Carvalho, J.G.Aparicio, R.Polikarpov, I.Leoni, J.Goldman, F.A.

(2000) J.Immunol. 165: 6422

  • Primary Citation of Related Structures:  1DN0

  • PubMed Abstract: 
  • Cold agglutinins (CAs) are IgM autoantibodies characterized by their ability to agglutinate in vitro RBC at low temperatures. These autoantibodies cause hemolytic anemia in patients with CA disease. Many diverse Ags are recognized by CAs, most freque ...

    Cold agglutinins (CAs) are IgM autoantibodies characterized by their ability to agglutinate in vitro RBC at low temperatures. These autoantibodies cause hemolytic anemia in patients with CA disease. Many diverse Ags are recognized by CAs, most frequently those belonging to the I/i system. These are oligosaccharides composed of repeated units of N:-acetyllactosamine, expressed on RBC. The three-dimensional structure of the Fab of KAU, a human monoclonal IgM CA with anti-I activity, was determined. The KAU combining site shows an extended cavity and a neighboring pocket. Residues from the hypervariable loops V(H)CDR3, V(L)CDR1, and V(L)CDR3 form the cavity, whereas the small pocket is defined essentially by residues from the hypervariable loops V(H)CDR1 and V(H)CDR2. This fact could explain the V(H)4-34 germline gene restriction among CA. The KAU combining site topography is consistent with one that binds a polysaccharide. The combining site overall dimensions are 15 A wide and 24 A long. Conservation of key binding site residues among anti-I/i CAs indicates that this is a common feature of this family of autoantibodies. We also describe the first high resolution structure of the human IgM C(H)1:C(L) domain. The structural analysis shows that the C(H)1-C(L) interface is mainly conserved during the isotype switch process from IgM to IgG1.


    Related Citations: 
    • Crystallization and Preliminary Diffraction Studies of a Human Fabm with Anti-I Activity
      Cauerhff, A.,Polikarpov, I.,Mathov, I.,Abatangelo, C.,Plotkin, L.,Goldbaum, F.A.,Leoni, J.
      (1998) Protein Pept.Lett. 5: 177
    • The Primary Structure of the Fab Fragment of Protein Kau, a Monoclonal Immunoglobulin M Cold Agglutinin
      Leoni, J.,Ghiso, J.,Goni, F.,Frangione, B.
      (1991) J.Biol.Chem. 266: 2836


    Organizational Affiliation

    Cátedra de Inmunología, Instituto de Estudios de la Inmunidad Humoral (IDEHU), Facultad de Farmacia y Bioquímica UBA, Buenos Aires, Argentina.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IGM KAPPA CHAIN V-III (KAU COLD AGGLUTININ)
A, C
215Homo sapiensGene Names: IGK@
Find proteins for Q6PJF2 (Homo sapiens)
Go to UniProtKB:  Q6PJF2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IGM FAB REGION IV-J(H4)-C (KAU COLD AGGLUTININ)
B, D
232N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FUC
Query on FUC

Download SDF File 
Download CCD File 
B, D
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
B, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.216 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 115.660α = 90.00
b = 115.660β = 90.00
c = 174.950γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-09-14
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance