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 

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: 10.1016/j.bbagen.2012.08.016

  • 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 oligomer ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Antigen Binding Fragment, Immunoglobulin IgG - Heavy Chain
H
215N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Antigen Binding Fragment, Immunoglobulin IgG - Light Chain
L
213N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
L
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.197 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 132.934α = 90.00
b = 42.184β = 114.93
c = 86.179γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
d*TREKdata reduction
PHASERphasing
REFMACrefinement
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-09-27 
  • Released Date: 2012-10-31 
  • Deposition Author(s): Arai, H.
  • This entry supersedes: 3NL4

Revision History 

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