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 1.3 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: 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) ...

    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

    University of Washington University of Washington, Department of Global Health, Seattle, WA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
iv8 Heavy ChainA, E, J [auth K], O [auth P]131Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
glVRC01 Light ChainB, F, K [auth L], M [auth N]111Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
glVRC01 Heavy ChainC, G [auth H], H [auth I], L [auth M]141Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
iv8 Light ChainD, I [auth J], N [auth O], P [auth Q]125Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / 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] , NA [auth K] , OA [auth K] , S [auth A] , 
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
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth F] , BA [auth F] , CA [auth F] , CB [auth Q] , EA [auth H] , FA [auth H] , GA [auth I] , HA [auth J] , 
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
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
BB [auth P], PA [auth K]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
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