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: 1.9 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1126/science.aao3859
  • Primary Citation of Related Structures:  

  • 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 prot ...

    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

    St. Vincent's Clinical School, University of New South Wales Sydney, Sydney, Australia.,Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, New South Wales 2010, Australia. d.christ@garvan.org.au c.goodnow@garvan.org.au.,Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, New South Wales 2010, Australia.,Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 OQH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HyHEL10 heavy chain Fab fragment carrying three mutations; I29F, S52T, Y53F
A, C, E, G
213N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HyHEL10 light chain Fab fragment
B, D, F, H
213N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Lysozyme
I, J, K, L
129N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
B, D, F, H
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
C, E, H, J
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 88.650α = 90.00
b = 132.660β = 90.00
c = 199.110γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2018-04-11
    Type: Initial release
  • Version 1.1: 2018-05-30
    Type: Data collection, Database references