1NBV

AN AUTOANTIBODY TO SINGLE-STRANDED DNA: COMPARISON OF THE THREE-DIMENSIONAL STRUCTURES OF THE UNLIGANDED FAB AND A DEOXYNUCLEOTIDE-FAB COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.246 
  • R-Value Observed: 0.246 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

An autoantibody to single-stranded DNA: comparison of the three-dimensional structures of the unliganded Fab and a deoxynucleotide-Fab complex.

Herron, J.N.He, X.M.Ballard, D.W.Blier, P.R.Pace, P.E.Bothwell, A.L.Voss Jr., E.W.Edmundson, A.B.

(1991) Proteins 11: 159-175

  • DOI: 10.1002/prot.340110302
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Crystal structures of the Fabs from an autoantibody (BV04-01) with specificity for single-stranded DNA have been determined in the presence and absence of a trinucleotide of deoxythymidylic acid, d(pT)3. Formation of the ligand-protein complex was ac ...

    Crystal structures of the Fabs from an autoantibody (BV04-01) with specificity for single-stranded DNA have been determined in the presence and absence of a trinucleotide of deoxythymidylic acid, d(pT)3. Formation of the ligand-protein complex was accompanied by small adjustments in the orientations of the variable (VL and VH) domains. In addition, there were local conformational changes in the first hypervariable loop of the light chain and the third hypervariable loop of the heavy chain, which together with the domain shifts led to an improvement in the complementarity of nucleotide and Fab. The sugar-phosphate chain adopted an extended and "open" conformation, with the base, sugar, and phosphate components available for interactions with the protein. Nucleotide 1 (5'-end) was associated exclusively with the heavy chain, nucleotide 2 was shared by both heavy and light chains, and nucleotide 3 was bound by the light chain. The orientation of phosphate 1 was stabilized by hydrogen bonds with serine H52a and asparagine H53. Phosphate 2 formed an ion pair with arginine H52, but no other charge-charge interactions were observed. Insertion of the side chain of histidine L27d between nucleotides 2 and 3 resulted in a bend in the sugar-phosphate chain. The most dominant contacts with the protein involved the central thymine base, which was immobilized by cooperative stacking and hydrogen bonding interactions. This base was intercalated between a tryptophan ring (no. H100a) from the heavy chain and a tyrosine ring (no. L32) from the light chain. The resulting orientation of thymine was favorable for the simultaneous formation of two hydrogen bonds with the backbone carbonyl oxygen and the side chain hydroxyl group of serine L91 (the thymine atoms were the hydrogen on nitrogen 3 and keto oxygen 4).


    Related Citations: 
    • Crystallographic Characterization of the Fab Fragment of a Monoclonal Anti-Ss-DNA Antibody
      Gibson, A.L., Herron, J.N., Ballard, D.W., Voss, E.W., He, X.M., Patrick, V.A., Edmundson, A.B.
      (1985) Mol Immunol 22: 499

    Organizational Affiliation

    Department of Pharmaceutics, University of Utah, Salt Lake City 84108.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IGG2B-KAPPA BV04-01 FAB (LIGHT CHAIN)L219Mus musculusMutation(s): 0 
Gene Names: IgkcIgk-C
Find proteins for A2NHM3 (Mus musculus)
Explore A2NHM3 
Go to UniProtKB:  A2NHM3
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IGG2B-KAPPA BV04-01 FAB (HEAVY CHAIN)H219Mus musculusMutation(s): 0 
Gene Names: Igh-3
Find proteins for P01867 (Mus musculus)
Explore P01867 
Go to UniProtKB:  P01867
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.246 
  • R-Value Observed: 0.246 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.4α = 83.4
b = 43.7β = 89.4
c = 41.5γ = 84.4
Software Package:
Software NamePurpose
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other
  • Version 1.4: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.5: 2019-08-14
    Changes: Data collection, Refinement description