6OL5

Structure of iglb12 Fab in complex with anti-idiotype ib3 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Detection and activation of HIV broadly neutralizing antibody precursor B cells using anti-idiotypes.

Bancroft, T.DeBuysscher, B.L.Weidle, C.Schwartz, A.Wall, A.Gray, M.D.Feng, J.Steach, H.R.Fitzpatrick, K.S.Gewe, M.M.Skog, P.D.Doyle-Cooper, C.Ota, T.Strong, R.K.Nemazee, D.Pancera, M.Stamatatos, L.McGuire, A.T.Taylor, J.J.

(2019) J Exp Med 216: 2331-2347

  • DOI: https://doi.org/10.1084/jem.20190164
  • Primary Citation of Related Structures:  
    6OL5, 6OL6

  • PubMed Abstract: 

    Many tested vaccines fail to provide protection against disease despite the induction of antibodies that bind the pathogen of interest. In light of this, there is much interest in rationally designed subunit vaccines that direct the antibody response to protective epitopes. Here, we produced a panel of anti-idiotype antibodies able to specifically recognize the inferred germline version of the human immunodeficiency virus 1 (HIV-1) broadly neutralizing antibody b12 (iglb12). We determined the crystal structure of two anti-idiotypes in complex with iglb12 and used these anti-idiotypes to identify rare naive human B cells expressing B cell receptors with similarity to iglb12. Immunization with a multimerized version of this anti-idiotype induced the proliferation of transgenic murine B cells expressing the iglb12 heavy chain in vivo, despite the presence of deletion and anergy within this population. Together, our data indicate that anti-idiotypes are a valuable tool for the study and induction of potentially protective antibodies.


  • Organizational Affiliation

    Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ib3 Heavy Chain222Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ib3 Light Chain214Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
iglb12 Heavy ChainC [auth H]230Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
iglb12 Light ChainD [auth L]215Homo sapiensMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download Ideal Coordinates CCD File 
JA [auth H],
K [auth A]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
KA [auth H]
L [auth A]
LA [auth H]
M [auth A]
MA [auth H]
KA [auth H],
L [auth A],
LA [auth H],
M [auth A],
MA [auth H],
N [auth A],
NA [auth H],
O [auth A],
P [auth A],
SA [auth L],
TA [auth L],
UA [auth L],
W [auth B],
X [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth B]
OA [auth H]
PA [auth H]
Q [auth A]
QA [auth H]
AA [auth B],
OA [auth H],
PA [auth H],
Q [auth A],
QA [auth H],
R [auth A],
S [auth A],
VA [auth L],
WA [auth L],
XA [auth L],
Y [auth B],
YA [auth L],
Z [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NH4
Query on NH4

Download Ideal Coordinates CCD File 
BA [auth H]
CA [auth H]
DA [auth H]
E [auth A]
EA [auth H]
BA [auth H],
CA [auth H],
DA [auth H],
E [auth A],
EA [auth H],
F [auth A],
FA [auth H],
G [auth A],
GA [auth H],
H [auth A],
HA [auth H],
I [auth A],
IA [auth H],
J [auth A],
RA [auth L],
T [auth B],
U [auth B],
V [auth B]
AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.551α = 90
b = 75.551β = 90
c = 389.714γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI081625

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-08-07
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-23
    Changes: Data collection, Database references
  • Version 2.0: 2019-12-18
    Changes: Author supporting evidence, Polymer sequence
  • Version 2.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description