Experimental Data Snapshot

  • Resolution: 2 Å

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history


Protein-protein recognition: crystal structural analysis of a barnase-barstar complex at 2.0-A resolution.

Buckle, A.M.Schreiber, G.Fersht, A.R.

(1994) Biochemistry 33: 8878-8889

  • PubMed Abstract: 
  • We have solved, refined, and analyzed the 2.0-å resolution crystal structure of a 1:1 complex between the bacterial ribonuclease, barnase, and a Cys-->Ala(40,82) double mutant of its intracellular polypeptide inhibitor, barstar. Barstar inhibits barn ...

    We have solved, refined, and analyzed the 2.0-å resolution crystal structure of a 1:1 complex between the bacterial ribonuclease, barnase, and a Cys-->Ala(40,82) double mutant of its intracellular polypeptide inhibitor, barstar. Barstar inhibits barnase by sterically blocking the active site with a helix and adjacent loop segment. Almost half of the 14 hydrogen bonds between barnase and barstar involve two charged residues, and a third involve one charged partner. The electrostatic contribution to the overall binding energy is considerably greater than for other protein-protein interactions. Consequently, the very high rate constant for the barnase-barstar association (10(8) s-1 M-1) is most likely due to electrostatic steering effects. The barnase active-site residue His102 is located in a pocket on the surface of barstar, and its hydrogen bonds with Asp39 and Gly31 residues of barstar are directly responsible for the pH dependence of barnase-barstar binding. There is a high degree of complementarity both of the shape and of the charge of the interacting surfaces, but neither is perfect. The surface complementarity is slightly poorer than in protease-inhibitor complexes but a little better than in antibody-antigen interactions. However, since the burial of solvent in the barnase-barstar interface improves the fit significantly by filling in the majority of gaps, as well as stabilizing unfavorable electrostatic interactions, its role seems to be more important than in other protein-protein complexes. The electrostatic interactions between barnase and barstar are very similar to those between barnase and the tetranucleotide d(CGAC). In the barnase-barstar complex, the two phosphate-binding sites in the barnase active site are occupied by Asp39 and Gly43 of barstar. However, barstar has no equivalent for a guanine base of an RNA substrate, resulting in the occupation of the guanine recognition site in the barnase-barstar complex by nine ordered water molecules. Upon barnase-barstar binding, entropy losses resulting from the immobilization of segments of the protein chain and the energetic costs of conformational changes are minimized due to the essentially preformed active site of barnase. However, a certain degree of flexibility within the barnase active site is required to allow for the structural differences between barnase-barstar binding and barnase-RNA binding. A comparison between the bound and the free barstar structure shows that the overall structural response to barnase-binding is significant. This response can be best described as outwardly oriented, rigid-body movements of the four alpha-helices of barstar, resulting in the structure of bound barstar being somewhat expanded.

    Related Citations: 
    • Interaction of Barnase with its Polypeptide Inhibitor Barstar Studied by Protein Engineering
      Schreiber, G.,Fersht, A.R.
      (1993) Biochemistry 32: 5145
    • Recognition between a Bacterial Ribonuclease, Barnase, and its Natural Inhibitor, Barstar
      Guillet, V.,Lapthorn, A.,Hartley, R.W.,Mauguen, Y.
      (1993) Structure 1: 165
    • Stability and Function: Two Constraints in the Evolution of Barstar and Other Proteins
      Schreiber, G.,Buckle, A.M.,Fersht, A.R.
      (1994) Structure 2: 945
    • Molecular Structures of a New Family of Ribonucleases
      Mauguen, Y.,Hartley, R.W.,Dodson, E.J.,Dodson, G.G.,Bricogne, G.,Chothia, C.,Jack, A.
      (1982) Nature 297: 162

    Organizational Affiliation

    Cambridge Centre for Protein Engineering, Medical Research Council Centre, U.K.


Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
A, B, C
110Bacillus amyloliquefaciensMutation(s): 0 
EC: 3.1.27.-
Find proteins for P00648 (Bacillus amyloliquefaciens)
Go to UniProtKB:  P00648
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
D, E, F
89Bacillus amyloliquefaciensMutation(s): 0 
Find proteins for P11540 (Bacillus amyloliquefaciens)
Go to UniProtKB:  P11540
Experimental Data & Validation

Experimental Data

  • Resolution: 2 Å
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 207.250α = 90.00
b = 43.860β = 107.76
c = 84.710γ = 90.00
Software Package:
Software NamePurpose

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-06-22
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other