4HBC

Crystal structure of a conformation-dependent rabbit IgG Fab specific for amyloid prefibrillar oligomers

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

Crystal structure of a conformation-dependent rabbit IgG Fab specific for amyloid prefibrillar oligomers.

Arai, H., Glabe, C., Luecke, H.

(2012) Biochim Biophys Acta 1820: 1908-1914

  • DOI: https://doi.org/10.1016/j.bbagen.2012.08.016
  • Primary Citation of Related Structures:  
    4HBC

  • PubMed Abstract: 

    Although rabbit antibodies are widely used in research, no structures of rabbit antigen-binding fragments (Fab) have been reported. M204 is a rabbit monoclonal antibody that recognizes a generic epitope that is common to prefibrillar amyloid oligomers formed from many different amyloidogenic sequences. Amyloid oligomers are widely suspected to be a primary causative agent of pathogenesis in several age-related neurodegenerative diseases, such as Alzheimer's disease. The detailed structure of these amyloid oligomers is not known nor is the mechanism for the recognition of the generic epitope by conformation-dependent monoclonal antibodies.

    • Organizational Affiliation: 

    Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Antigen Binding Fragment, Immunoglobulin IgG - Heavy ChainA [auth H]215Oryctolagus cuniculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Antigen Binding Fragment, Immunoglobulin IgG - Light ChainB [auth L]213Oryctolagus cuniculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
C [auth L]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.934α = 90
b = 42.184β = 114.93
c = 86.179γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
d*TREKdata reduction
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2012-10-31 
    • Deposition Author(s): Arai, H.
  • This entry supersedes: 3NL4

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-31
    Type: Initial release