Skip to main content

 6OL7 | pdb_00006ol7

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 (Depositor), 0.224 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6OL7

This is version 1.5 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 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.

Macromolecule Content 

  • Total Structure Weight: 223.43 kDa 
  • Atom Count: 15,686 
  • Modeled Residue Count: 1,851 
  • Deposited Residue Count: 2,032 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  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:|  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:|  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:|  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 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
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
  • Version 1.5: 2024-11-20
    Changes: Structure summary