6P4C | pdb_00006p4c

HyHEL10 Fab carrying four heavy chain mutations (HyHEL10-4x): L4F, Y33H, S56N, and Y58F


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.223 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 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 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.

Macromolecule Content 

  • Total Structure Weight: 48.15 kDa 
  • Atom Count: 3,367 
  • Modeled Residue Count: 420 
  • Deposited Residue Count: 437 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HyHEL10 Fab light chainA [auth L]214Mus musculusMutation(s): 0 
UniProt
Find proteins for A0A0E4B213 (Mus musculus)
Explore A0A0E4B213 
Go to UniProtKB:  A0A0E4B213
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0E4B213
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
HyHEL10 Fab heavy chainB [auth H]223Mus musculusMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.223 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.556α = 90
b = 40.156β = 107.57
c = 93.649γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
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
  • Version 1.3: 2024-11-06
    Changes: Structure summary