6OL7

Crystal structure of glVRC01 scFv in complex with anti-idiotype iv8 scFv


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Anti-idiotypic antibodies elicit anti-HIV-1-specific B cell responses.

Dosenovic, P.Pettersson, A.K.Wall, A.Thientosapol, E.S.Feng, J.Weidle, C.Bhullar, K.Kara, E.E.Hartweger, H.Pai, J.A.Gray, M.D.Parks, K.R.Taylor, J.J.Pancera, M.Stamatatos, L.Nussenzweig, M.C.McGuire, A.T.

(2019) J Exp Med 216: 2316-2330

  • DOI: https://doi.org/10.1084/jem.20190446
  • Primary Citation of Related Structures:  
    6OL7

  • PubMed Abstract: 

    Human anti-HIV-1 broadly neutralizing antibodies (bNAbs) protect against infection in animal models. However, bNAbs have not been elicited by vaccination in diverse wild-type animals or humans, in part because B cells expressing the precursors of these antibodies do not recognize most HIV-1 envelopes (Envs). Immunogens have been designed that activate these B cell precursors in vivo, but they also activate competing off-target responses. Here we report on a complementary approach to expand specific B cells using an anti-idiotypic antibody, iv8, that selects for naive human B cells expressing immunoglobulin light chains with 5-amino acid complementarity determining region 3s, a key feature of anti-CD4 binding site (CD4bs)-specific VRC01-class antibodies. In mice, iv8 induced target cells to expand and mature in the context of a polyclonal immune system and produced serologic responses targeting the CD4bs on Env. In summary, the results demonstrate that an anti-idiotypic antibody can specifically recognize and expand rare B cells that express VRC01-class antibodies against HIV-1.


  • Organizational Affiliation

    Laboratory of Molecular Immunology, The Rockefeller University, New York, NY.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
iv8 Heavy ChainA,
E,
J [auth K],
O [auth P]
131Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
glVRC01 Light ChainB,
F,
K [auth L],
M [auth N]
111Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
glVRC01 Heavy ChainC,
G [auth H],
H [auth I],
L [auth M]
141Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
iv8 Light ChainD,
I [auth J],
N [auth O],
P [auth Q]
125Mus 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
PEG
Query on PEG

Download Ideal Coordinates CCD File 
AB [auth O]
DA [auth F]
DB [auth Q]
IA [auth J]
JA [auth J]
AB [auth O],
DA [auth F],
DB [auth Q],
IA [auth J],
JA [auth J],
NA [auth K],
OA [auth K],
S [auth A],
TA [auth M],
YA [auth N]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth F]
BA [auth F]
CA [auth F]
CB [auth Q]
EA [auth H]
AA [auth F],
BA [auth F],
CA [auth F],
CB [auth Q],
EA [auth H],
FA [auth H],
GA [auth I],
HA [auth J],
KA [auth K],
LA [auth K],
MA [auth K],
Q [auth A],
QA [auth L],
R [auth A],
RA [auth M],
SA [auth M],
T [auth B],
U [auth B],
UA [auth N],
V [auth B],
VA [auth N],
W [auth B],
WA [auth N],
X [auth C],
XA [auth N],
Y [auth D],
Z [auth D],
ZA [auth O]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
BB [auth P],
PA [auth K]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.583α = 85.49
b = 107.937β = 80.28
c = 116.961γ = 84.17
Software Package:
Software NamePurpose
PHENIXrefinement
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 StatesHIVRAD/1P01AI138212
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI081625
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP01 AI138212

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 1.3: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description