5JOR | pdb_00005jor

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 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5JOR

This is version 1.3 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 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. 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.

Macromolecule Content 

  • Total Structure Weight: 213.3 kDa 
  • Atom Count: 14,568 
  • Modeled Residue Count: 1,708 
  • Deposited Residue Count: 1,872 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
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 
Find similar proteins by:|  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 

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 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
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
  • Version 1.3: 2024-12-25
    Changes: Advisory, Derived calculations, Structure summary