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 5VJQ | pdb_00005vjq

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 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5VJQ

This is version 1.5 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 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.

Macromolecule Content 

  • Total Structure Weight: 244.89 kDa 
  • Atom Count: 17,903 
  • Modeled Residue Count: 2,186 
  • Deposited Residue Count: 2,220 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  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
UniProt
Find proteins for P01868 (Mus musculus)
Explore P01868 
Go to UniProtKB:  P01868
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01868
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
HyHEL10 light chain Fab fragmentB,
E [auth D],
H [auth F],
K [auth H]
213Mus musculusMutation(s): 0 
UniProt
Find proteins for A0A125T904 (Mus musculus)
Explore A0A125T904 
Go to UniProtKB:  A0A125T904
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A125T904
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
LysozymeC [auth I],
F [auth J],
I [auth K],
L
129Anas platyrhynchosMutation(s): 0 
EC: 3.2.1.17
UniProt
Find proteins for P00705 (Anas platyrhynchos)
Explore P00705 
Go to UniProtKB:  P00705
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00705
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 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
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
  • Version 1.5: 2024-10-30
    Changes: Structure summary