1HH9

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.333 
  • R-Value Work: 0.282 
  • R-Value Observed: 0.282 

wwPDB Validation   3D Report Full Report


This is version 1.5 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:  
    1HH6, 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 antibody CB4-1 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
IGG2A KAPPA ANTIBODY CB41 (LIGHT CHAIN)A214Mus musculusMutation(s): 0 
Gene Names: Igkc
UniProt
Find proteins for P01837 (Mus musculus)
Explore P01837 
Go to UniProtKB:  P01837
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
IGG2A KAPPA ANTIBODY CB41 (HEAVY CHAIN)B213Mus musculusMutation(s): 0 
UniProt
Find proteins for P01864 (Mus musculus)
Explore P01864 
Go to UniProtKB:  P01864
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PEP-2C12synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.333 
  • R-Value Work: 0.282 
  • R-Value Observed: 0.282 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.72α = 90
b = 102.72β = 90
c = 295.24γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-01-12
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 1.4: 2019-07-24
    Changes: Data collection
  • Version 1.5: 2019-10-09
    Changes: Data collection, Other, Source and taxonomy