Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 97.34 kDa 
• Atom Count: 6771 
• Residue Count: 864 
• Unique protein chains: 2

6CXL

anti-HIV-1 Fab 2G12 in complex with glycopeptide 10F5

• DOI: 10.2210/pdb6CXL/pdb

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


• Deposited: 2018-04-03 Released: 2019-02-20 
• Deposition Author(s): Stanfield, R.L., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.59 Å
• R-Value Free: 0.248 
• R-Value Work: 0.219 
• R-Value Observed: 0.220 

Literature

Oligomannose Glycopeptide Conjugates Elicit Antibodies Targeting the Glycan Core Rather than Its Extremities.

Nguyen, D.N., Xu, B., Stanfield, R.L., Bailey, J.K., Horiya, S., Temme, J.S., Leon, D.R., LaBranche, C.C., Montefiori, D.C., Costello, C.E., Wilson, I.A., Krauss, I.J.

(2019) ACS Cent Sci 5: 237-249

• PubMed: 30834312 
• DOI: 10.1021/acscentsci.8b00588
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Up to ∼20% of HIV-infected individuals eventually develop broadly neutralizing antibodies (bnAbs), and many of these antibodies (∼40%) target a region of dense high-mannose glycosylation on gp120 of the HIV envelope protein, known as the "high-mannose patch" (HMP). Thus, there have been numerous attempts to develop glycoconjugate vaccine immunogens that structurally mimic the HMP and might elicit bnAbs targeting this conserved neutralization epitope. Herein, we report on the immunogenicity of glycopeptides, designed by in vitro selection, that bind tightly to anti-HMP antibody 2G12. By analyzing the fine carbohydrate specificity of rabbit antibodies elicited by these immunogens, we found that they differ from some natural human bnAbs, such as 2G12 and PGT128, in that they bind primarily to the core structures within the glycan, rather than to the Manα1 → 2Man termini (2G12) or to the whole glycan (PGT128). Antibody specificity for the glycan core may result from extensive serum mannosidase trimming of the immunogen in the vaccinated animals. This finding has broad implications for vaccine design aiming to target glycan-dependent HIV neutralizing antibodies.

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Organizational Affiliation: 

Department of Chemistry, Brandeis University, Waltham, Massachusetts 02454-9110, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
anti-HIV-1 Fab 2G12 light chain	K, L	213	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
anti-HIV-1 Fab 2G12 heavy chain	H, M	224	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BMA	H, M	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
MAN	H, M	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.59 Å
• R-Value Free: 0.248 
• R-Value Work: 0.219 
• R-Value Observed: 0.220 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.641	α = 90
b = 146.308	β = 90
c = 148.213	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-04-03 
• Released Date: 2019-02-20 
Deposition Author(s): Stanfield, R.L., Wilson, I.A.

Revision History 

• Version 1.0: 2019-02-20
  Type: Initial release
  
• Version 1.1: 2019-03-20
  Changes: Data collection, Database references