1HH6

ANTI-P24 (HIV-1) FAB FRAGMENT CB41 COMPLEXED WITH A PEPTIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.338 
  • R-Value Work: 0.294 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Evolutionary Transition Pathways for Changing Peptide Ligand Specificity and Structure

Hoffmuller, U.Knaute, T.Hahn, M.Hohne, W.Schneider-Mergener, J.Kramer, A.

(2000) Embo J. 19: 4866

  • DOI: 10.1093/emboj/19.18.4866
  • Primary Citation of Related Structures:  1HH9

  • PubMed Abstract: 
  • We identified evolutionary pathways for the inter- conversion of three sequentially and structurally unrelated peptides, GATPEDLNQKL, GLYEWGGARI and FDKEWNLIEQN, binding to the same site of the hypervariable region of the anti-p24 (HIV-1) monoclonal ...

    We identified evolutionary pathways for the inter- conversion of three sequentially and structurally unrelated peptides, GATPEDLNQKL, GLYEWGGARI and FDKEWNLIEQN, binding to the same site of the hypervariable region of the anti-p24 (HIV-1) monoclonal antibody CB4-1. Conversion of these peptides into each other could be achieved in nine or 10 single amino acid substitution steps without loss of antibody binding. Such pathways were identified by analyzing all 7 620 480 pathways connecting 2560 different peptides, and testing them for CB4-1 binding. The binding modes of intermediate peptides of selected optimal pathways were characterized using complete sets of substitution analogs, revealing that a number of sequential substitutions accumulated without changing the pattern of key interacting residues. At a distinct step, however, one single amino acid exchange induces a sudden change in the binding mode, indicating a flip in specificity and conformation. Our data represent a model of how different specificities, structures and functions might evolve in protein-protein recognition.


    Related Citations: 
    • Crystallographic Analysis of Anti-P24 (HIV-1) Monoclonal Antibody Cross-Reactivity and Polyspecificity
      Keitel, T.,Kramer, A.,Wessner, H.,Scholz, C.,Schneider-Mergener, J.,Hohne, W.
      (1997) Cell 91: 811


    Organizational Affiliation

    Institut für Medizinische Immunologie and Institut für Biochemie, Universitätsklinikum Charité, Humboldt-Universität zu Berlin, Schumannstrasse 20/21, 10098 Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IGG2A KAPPA ANTIBODY CB41 (LIGHT CHAIN)
A
214Mus musculusN/A
Find proteins for P01837 (Mus musculus)
Go to UniProtKB:  P01837
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IGG2A KAPPA ANTIBODY CB41 (HEAVY CHAIN)
B
213Mus musculusN/A
Find proteins for P01864 (Mus musculus)
Go to UniProtKB:  P01864
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PEP-4
C
11N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.338 
  • R-Value Work: 0.294 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 102.960α = 90.00
b = 102.960β = 90.00
c = 294.090γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
AMoREphasing
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-01-26
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance