5VJQ

Complex between HyHEL10 Fab fragment heavy chain mutant (I29F, S52T, Y53F) and Pekin duck egg lysozyme isoform I (DEL-I)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Germinal center antibody mutation trajectories are determined by rapid self/foreign discrimination.

Burnett, D.L.Langley, D.B.Schofield, P.Hermes, J.R.Chan, T.D.Jackson, J.Bourne, K.Reed, J.H.Patterson, K.Porebski, B.T.Brink, R.Christ, D.Goodnow, C.C.

(2018) Science 360: 223-226

  • DOI: https://doi.org/10.1126/science.aao3859
  • Primary Citation of Related Structures:  
    5VJO, 5VJQ

  • PubMed Abstract: 

    Antibodies have the specificity to differentiate foreign antigens that mimic self antigens, but it remains unclear how such specificity is acquired. In a mouse model, we generated B cells displaying an antibody that cross-reacts with two related protein antigens expressed on self versus foreign cells. B cell anergy was imposed by self antigen but reversed upon challenge with high-density foreign antigen, leading to germinal center recruitment and antibody gene hypermutation. Single-cell analysis detected rapid selection for mutations that decrease self affinity and slower selection for epistatic mutations that specifically increase foreign affinity. Crystal structures revealed that these mutations exploited subtle topological differences to achieve 5000-fold preferential binding to foreign over self epitopes. Resolution of antigenic mimicry drove the optimal affinity maturation trajectory, highlighting the value of retaining self-reactive clones as substrates for protective antibody responses.


  • Organizational Affiliation

    Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, New South Wales 2010, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HyHEL10 heavy chain Fab fragment carrying three mutations; I29F, S52T, Y53FA,
D [auth C],
G [auth E],
J [auth G]
213Mus musculusMutation(s): 0 
Gene Names: IgG heavy chain
EC: 3.2.1.18
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HyHEL10 light chain Fab fragmentB,
E [auth D],
H [auth F],
K [auth H]
213Mus musculusMutation(s): 0 
Entity Groups  
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
LysozymeC [auth I],
F [auth J],
I [auth K],
L
129Anas platyrhynchosMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
N [auth C]
O [auth C]
P [auth C]
R [auth J]
S [auth E]
N [auth C],
O [auth C],
P [auth C],
R [auth J],
S [auth E],
V [auth H]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
M [auth B],
Q [auth D],
T [auth F],
U [auth H]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.65α = 90
b = 132.66β = 90
c = 199.11γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia--

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-11
    Type: Initial release
  • Version 1.1: 2018-05-30
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.3: 2020-01-29
    Changes: Derived calculations
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Refinement description