2EH8

Crystal structure of the complex of humanized KR127 fab and PRES1 peptide epitope


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Broadly neutralizing anti-hepatitis B virus antibody reveals a complementarity determining region H3 lid-opening mechanism

Chi, S.-W.Maeng, C.-Y.Kim, S.J.Oh, M.S.Ryu, C.J.Kim, S.-J.Han, K.-H.Hong, H.J.Ryu, S.-E.

(2007) Proc Natl Acad Sci U S A 104: 9230-9235

  • DOI: https://doi.org/10.1073/pnas.0701279104
  • Primary Citation of Related Structures:  
    2EH7, 2EH8

  • PubMed Abstract: 

    The humanized monoclonal antibody HzKR127 recognizes the preS1 domain of the human hepatitis B virus surface proteins with a broadly neutralizing activity in vivo. We present the crystal structures of HzKR127 Fab and its complex with a major epitope peptide. In the complex structure, the bound peptide forms a type IV beta-turn followed by 3(10) helical turn, the looped-out conformation of which provides a structural basis for broad neutralization. Upon peptide binding, the antibody undergoes a dramatic complementarity determining region H3 lid opening. To understand the structural implication of the virus neutralization, we carried out comprehensive alanine-scanning mutagenesis of all complementarity determining region residues in HzKR127 Fab. The functional mapping of the antigen-combining site demonstrates the specific roles of major binding determinants in antigen binding, contributing to the rational design for maximal humanization and affinity maturation of the antibody.


  • Organizational Affiliation

    Center for Cellular Switch Protein Structure, Molecular Cancer Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-333, Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HUMANIZED KR127 FAB, LIGHT CHAINA [auth L]218Mus musculusMutation(s): 0 
Gene Names: HUMANIZED KR127
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HUMANIZED KR127 FAB, HEAVY CHAINB [auth H]218Mus musculusMutation(s): 0 
Gene Names: HUMANIZED KR127
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PreS1/PreS2/surface proteinC [auth P]11N/AMutation(s): 0 
UniProt
Find proteins for Q2EID8 (Hepatitis B virus)
Explore Q2EID8 
Go to UniProtKB:  Q2EID8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2EID8
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.34α = 90
b = 61.27β = 93.25
c = 83.54γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-01-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-11
    Changes: Refinement description
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Refinement description