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 1.1 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: 10.1172/JCI91192
  • Primary Citation of Related Structures:  
    5JOP, 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 ...

    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.

    Organizational Affiliation: 

    Department of Urology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University , Hangzhou , China .



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fab14.22 heavy chainA [auth B],
G [auth D],
C [auth F],
D [auth H]		249Mus musculusMutation(s): 0 
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Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fab 14.22 light chainB [auth A],
F [auth C],
H [auth E],
E [auth L]		219Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / 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		 Ligand Interaction
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		 Ligand Interaction
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		 Ligand Interaction
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

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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