6P4B

HyHEL10 fab variant HyHEL10-4x (heavy chain mutations L4F, Y33H, S56N, and Y58F) bound to hen egg lysozyme variant HEL2x-flex (mutations R21Q, R73E, C76S, and C94S)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report

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This is version 1.2 of the entry. See complete history


Literature

Conformational diversity facilitates antibody mutation trajectories and discrimination between foreign and self-antigens.

Burnett, D.L.Schofield, P.Langley, D.B.Jackson, J.Bourne, K.Wilson, E.Porebski, B.T.Buckle, A.M.Brink, R.Goodnow, C.C.Christ, D.

(2020) Proc Natl Acad Sci U S A 117: 22341-22350

  • DOI: https://doi.org/10.1073/pnas.2005102117
  • Primary Citation of Related Structures:  
    6P4A, 6P4B, 6P4C, 6P4D

  • PubMed Abstract: 

    Conformational diversity and self-cross-reactivity of antigens have been correlated with evasion from neutralizing antibody responses. We utilized single cell B cell sequencing, biolayer interferometry and X-ray crystallography to trace mutation selection pathways where the antibody response must resolve cross-reactivity between foreign and self-proteins bearing near-identical contact surfaces, but differing in conformational flexibility. Recurring antibody mutation trajectories mediate long-range rearrangements of framework (FW) and complementarity determining regions (CDRs) that increase binding site conformational diversity. These antibody mutations decrease affinity for self-antigen 19-fold and increase foreign affinity 67-fold, to yield a more than 1,250-fold increase in binding discrimination. These results demonstrate how conformational diversity in antigen and antibody does not act as a barrier, as previously suggested, but rather facilitates high affinity and high discrimination between foreign and self.


  • Organizational Affiliation

    Garvan Institute of Medical Research, University of New South Wales (UNSW) Sydney, Darlinghurst, NSW 2010, Australia.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HyHEL10 Fab light chainA [auth L],
D [auth A]
214Mus musculusMutation(s): 0 
UniProt
Find proteins for A0A0E4B213 (Mus musculus)
Explore A0A0E4B213 
Go to UniProtKB:  A0A0E4B213
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UniProt GroupA0A0E4B213
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HyHEL10 Fab heavy chainB [auth H],
E [auth B]
223Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme CC,
F [auth D]
129Gallus gallusMutation(s): 4 
Gene Names: LYZ
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Entity Groups  
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UniProt GroupP00698
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.397α = 90
b = 65.722β = 98.48
c = 137.128γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-27
    Type: Initial release
  • Version 1.1: 2020-12-16
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description