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 2.1 of the entry. See complete history


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:  
    1DN0, 1QLR

  • 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 those belonging to the I/i system ...

    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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
IGM KAPPA CHAIN V-III (KAU COLD AGGLUTININ)A, C215Homo sapiensMutation(s): 0 
Gene Names: IGK@
UniProt
Find proteins for Q6PJF2 (Homo sapiens)
Explore Q6PJF2 
Go to UniProtKB:  Q6PJF2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6PJF2
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
IGM FAB REGION IV-J(H4)-C (KAU COLD AGGLUTININ)B, D232Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranoseE, F 2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G86851RC
GlyCosmos:  G86851RC
GlyGen:  G86851RC
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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 2.1: 2021-08-11
    Changes: Database references, Derived calculations, Structure summary