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



Literature

Three-dimensional structure of the Fab from a human IgM cold agglutinin.

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

(2000) J Immunol 165: 6422-6428

  • DOI: 10.4049/jimmunol.165.11.6422
  • Primary Citation of Related Structures:  
    1QLR, 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 frequently ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
IGM KAPPA CHAIN V-III (KAU COLD AGGLUTININ) AC215Homo sapiensMutation(s): 0 
Gene Names: IGK@
Find proteins for Q6PJF2 (Homo sapiens)
Explore Q6PJF2 
Go to UniProtKB:  Q6PJF2
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
IGM FAB REGION IV-J(H4)-C (KAU COLD AGGLUTININ) BD232Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, F
2 N-Glycosylation Oligosaccharides 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 = 115.66α = 90
b = 115.66β = 90
c = 174.95γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-09-14
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-10-09
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary