4K3D

Crystal structure of bovine antibody BLV1H12 with ultralong CDR H3

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

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This is version 1.1 of the entry. See complete history. 


Literature

Reshaping antibody diversity.

Wang, F., Ekiert, D.C., Ahmad, I., Yu, W., Zhang, Y., Bazirgan, O., Torkamani, A., Raudsepp, T., Mwangi, W., Criscitiello, M.F., Wilson, I.A., Schultz, P.G., Smider, V.V.

(2013) Cell 153: 1379-1393

  • DOI: 10.1016/j.cell.2013.04.049
  • Primary Citation of Related Structures:  
    4K3D, 4K3E

  • PubMed Abstract: 

    • Some species mount a robust antibody response despite having limited genome-encoded combinatorial diversity potential. Cows are unusual in having exceptionally long CDR H3 loops and few V regions, but the mechanism for creating diversity is not understood ...

    Some species mount a robust antibody response despite having limited genome-encoded combinatorial diversity potential. Cows are unusual in having exceptionally long CDR H3 loops and few V regions, but the mechanism for creating diversity is not understood. Deep sequencing reveals that ultralong CDR H3s contain a remarkable complexity of cysteines, suggesting that disulfide-bonded minidomains may arise during repertoire development. Indeed, crystal structures of two cow antibodies reveal that these CDR H3s form a very unusual architecture composed of a β strand "stalk" that supports a structurally diverse, disulfide-bonded "knob" domain. Diversity arises from somatic hypermutation of an ultralong DH with a severe codon bias toward mutation to cysteine. These unusual antibodies can be elicited to recognize defined antigens through the knob domain. Thus, the bovine immune system produces an antibody repertoire composed of ultralong CDR H3s that fold into a diversity of minidomains generated through combinations of somatically generated disulfides.

    Organizational Affiliation: 

    Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BOVINE ANTIBODY WITH ULTRALONG CDR H3, HEAVY CHAINA [auth H],
C [auth I]		280Bos taurusMutation(s): 0 
Gene Names: IGH
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
BOVINE ANTIBODY WITH ULTRALONG CDR H3, LIGHT CHAINB [auth L],
D [auth M]		216Bos taurusMutation(s): 0 
Gene Names: IGL, IGL@
UniProt
Find proteins for Q3T101 (Bos taurus)
Explore Q3T101 
Go to UniProtKB:  Q3T101
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3T101
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT
Download Ideal Coordinates CCD File 
F [auth H]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N		 Ligand Interaction
K
Query on K
Download Ideal Coordinates CCD File 
E [auth H]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA		A [auth H],
C [auth I]		L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.41α = 90
b = 127.6β = 90
c = 127.87γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
XPREPdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-19
    Type: Initial release
  • Version 1.1: 2013-07-03
    Changes: Database references