5ILT

Crystal structure of bovine Fab A01


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Conservation and diversity in the ultralong third heavy-chain complementarity-determining region of bovine antibodies.

Stanfield, R.L.Wilson, I.A.Smider, V.V.

(2016) Sci Immunol 1: aaf7962-aaf7962

  • DOI: 10.1126/sciimmunol.aaf7962

  • PubMed Abstract: 
  • Antibodies provide a broad defense against a vast array of antigens; however, the structural features that contribute to this diverse antigen recognition vary in different vertebrates. In cows, a subset of antibodies have an exceptionally long third ...

    Antibodies provide a broad defense against a vast array of antigens; however, the structural features that contribute to this diverse antigen recognition vary in different vertebrates. In cows, a subset of antibodies have an exceptionally long third heavy-chain complementarity-determining region (CDR H3) that is highly variable in sequence and includes multiple cysteines. These long CDR H3s (up to 69 residues) fold into a long stalk atop which sits a knob domain that is located far from the antibody surface. We have determined crystal structures of three bovine Fabs to decipher the conserved and variable features of ultralong CDR H3s that lead to diversity in antigen recognition. Despite high sequence variability, the stalks adopt a conserved β-ribbon structure, whereas the knob regions share a conserved β sheet that serves as a scaffold for two connecting loops of variable length and conformation, as well as one conserved disulfide. Variation in patterns and connectivity of the remaining disulfides contribute to the structural diversity of the knob. The unusual architecture of these ultralong bovine CDR H3s for generating diversity is unique in adaptive immune systems and may inform efforts in antibody engineering.


    Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
bovine Fab A01 light chain
L
216N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
bovine Fab A01 heavy chain
H
271N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.211 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 80.490α = 90.00
b = 72.490β = 107.31
c = 87.420γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-08-24
    Type: Initial release
  • Version 1.1: 2016-09-14
    Type: Database references
  • Version 1.2: 2018-03-14
    Type: Database references, Derived calculations