6OL7

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

• PDB DOI:  https://doi.org/10.2210/pdb6OL7/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2019-04-15 Released: 2019-07-24 
• Deposition Author(s): Weidle, C., Pancera, M.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

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 

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

• PubMed: 31345931 
• 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: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 4 assigned by authors.

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
iv8 Heavy Chain	A, E, J [auth K], O [auth P]	131	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
glVRC01 Light Chain	B, F, K [auth L], M [auth N]	111	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
glVRC01 Heavy Chain	C, G [auth H], H [auth I], L [auth M]	141	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
iv8 Light Chain	D, I [auth J], N [auth O], P [auth Q]	125	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	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	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	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 = 51.583	α = 85.49
b = 107.937	β = 80.28
c = 116.961	γ = 84.17

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-07-24 
Deposition Author(s): Weidle, C., Pancera, M.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HIVRAD/1P01AI138212
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI081625
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	P01 AI138212

Revision History  

• 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