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 1.2 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: 10.1073/pnas.0701279104
  • Primary Citation of Related Structures:  
    2EH8, 2EH7

  • 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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HUMANIZED KR127 FAB, LIGHT CHAINA [auth L]218Mus musculusMutation(s): 0 
Gene Names: HUMANIZED KR127
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HUMANIZED KR127 FAB, HEAVY CHAINB [auth H]218Mus musculusMutation(s): 0 
Gene Names: HUMANIZED KR127
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence 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
Protein Feature View
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  • 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

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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