5JOR

Crystal structure of unbound anti-glycan antibody Fab14.22 at 2.2 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

T cells control the generation of nanomolar-affinity anti-glycan antibodies.

Polonskaya, Z.Deng, S.Sarkar, A.Kain, L.Comellas-Aragones, M.McKay, C.S.Kaczanowska, K.Holt, M.McBride, R.Palomo, V.Self, K.M.Taylor, S.Irimia, A.Mehta, S.R.Dan, J.M.Brigger, M.Crotty, S.Schoenberger, S.P.Paulson, J.C.Wilson, I.A.Savage, P.B.Finn, M.G.Teyton, L.

(2017) J Clin Invest 127: 1491-1504

  • DOI: https://doi.org/10.1172/JCI91192
  • Primary Citation of Related Structures:  
    5JOR

  • PubMed Abstract: 

    Vaccines targeting glycan structures at the surface of pathogenic microbes must overcome the inherent T cell-independent nature of immune responses against glycans. Carbohydrate conjugate vaccines achieve this by coupling bacterial polysaccharides to a carrier protein that recruits heterologous CD4 T cells to help B cell maturation. Yet they most often produce low- to medium-affinity immune responses of limited duration in immunologically fit individuals and disappointing results in the elderly and immunocompromised patients. Here, we hypothesized that these limitations result from suboptimal T cell help. To produce the next generation of more efficacious conjugate vaccines, we have explored a synthetic design aimed at focusing both B cell and T cell recognition to a single short glycan displayed at the surface of a virus-like particle. We tested and established the proof of concept of this approach for 2 serotypes of Streptococcus pneumoniae. In both cases, these vaccines elicited serotype-specific, protective, and long-lasting IgG antibodies of nanomolar affinity against the target glycans in mice. We further identified a requirement for CD4 T cells in the anti-glycan antibody response. Our findings establish the design principles for improved glycan conjugate vaccines. We surmise that the same approach can be used for any microbial glycan of interest.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fab14.22 heavy chainA [auth B],
C [auth F],
D [auth H],
G [auth D]
249Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab 14.22 light chainB [auth A],
E [auth L],
F [auth C],
H [auth E]
219Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
FB [auth C]
LA [auth F]
MA [auth F]
N [auth B]
NB [auth D]
FB [auth C],
LA [auth F],
MA [auth F],
N [auth B],
NB [auth D],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
RA [auth H],
S [auth B],
SA [auth H],
WB [auth E],
Y [auth A],
ZA [auth L]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
CB [auth C]
DB [auth C]
EB [auth C]
HA [auth F]
IA [auth F]
CB [auth C],
DB [auth C],
EB [auth C],
HA [auth F],
IA [auth F],
JA [auth F],
K [auth B],
KA [auth F],
L [auth B],
M [auth B],
MB [auth D],
PA [auth H],
QA [auth H],
UB [auth E],
VB [auth E],
W [auth A],
X [auth A],
XA [auth L],
YA [auth L]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth F]
AB [auth C]
BA [auth F]
BB [auth C]
CA [auth F]
AA [auth F],
AB [auth C],
BA [auth F],
BB [auth C],
CA [auth F],
DA [auth F],
EA [auth F],
FA [auth F],
GA [auth F],
GB [auth D],
HB [auth D],
I [auth B],
IB [auth D],
J [auth B],
JB [auth D],
KB [auth D],
LB [auth D],
NA [auth H],
OA [auth H],
OB [auth E],
PB [auth E],
QB [auth E],
RB [auth E],
SB [auth E],
T [auth A],
TA [auth L],
TB [auth E],
U [auth A],
UA [auth L],
V [auth A],
VA [auth L],
WA [auth L],
Z [auth F]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.613α = 90
b = 75.992β = 100.58
c = 122.946γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2017-04-12
    Changes: Database references
  • Version 1.2: 2023-09-27
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description