Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 96.17 kDa 
• Atom Count: 7891 
• Residue Count: 863 
• Unique protein chains: 2

3OAZ

A non-self sugar mimic of the HIV glycan shield shows enhanced antigenicity

• DOI: 10.2210/pdb3OAZ/pdb

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


• Deposited: 2010-08-06 Released: 2011-01-12 
• Deposition Author(s): Doores, K.J., Fulton, Z., Hong, V., Patel, M.K., Scanlan, C.N., Wormald, M.R., Finn, M.G., Burton, D.R., Wilson, I.A., Davis, B.G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.217 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 

Literature

A nonself sugar mimic of the HIV glycan shield shows enhanced antigenicity.

Doores, K.J., Fulton, Z., Hong, V., Patel, M.K., Scanlan, C.N., Wormald, M.R., Finn, M.G., Burton, D.R., Wilson, I.A., Davis, B.G.

(2010) Proc Natl Acad Sci U S A 107: 17107-17112

• PubMed: 20852065 
• DOI: 10.1073/pnas.1002717107
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Antibody 2G12 uniquely neutralizes a broad range of HIV-1 isolates by binding the high-mannose glycans on the HIV-1 surface glycoprotein, gp120. Antigens that resemble these natural epitopes of 2G12 would be highly desirable components for an HIV-1 vaccine. However, host-produced (self)-carbohydrate motifs have been unsuccessful so far at eliciting 2G12-like antibodies that cross-react with gp120. Based on the surprising observation that 2G12 binds nonproteinaceous monosaccharide D-fructose with higher affinity than D-mannose, we show here that a designed set of nonself, synthetic monosaccharides are potent antigens. When introduced to the terminus of the D1 arm of protein glycans recognized by 2G12, their antigenicity is significantly enhanced. Logical variation of these unnatural sugars pinpointed key modifications, and the molecular basis of this increased antigenicity was elucidated using high-resolution crystallographic analyses. Virus-like particle protein conjugates containing such nonself glycans are bound more tightly by 2G12. As immunogens they elicit higher titers of antibodies than those immunogenic conjugates containing the self D1 glycan motif. These antibodies generated from nonself immunogens also cross-react with this self motif, which is found in the glycan shield, when it is presented in a range of different conjugates and glycans. However, these antibodies did not bind this glycan motif when present on gp120.

---

Organizational Affiliation: 

Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, United Kingdom.

Macromolecules

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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Fab 2G12, heavy chain	H, M	223	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2M5	H, M	methyl 7-deoxy-L-glycero-alpha-D-manno-heptopyranoside C8 H16 O6 PNWOVLBMFHSUMR-IHKZFYOVSA-N
GOL	H, K, L, M	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	H, K, L, M	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.217 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.623	α = 90
b = 72.092	β = 95.78
c = 84.074	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-08-06 
• Released Date: 2011-01-12 
Deposition Author(s): Doores, K.J., Fulton, Z., Hong, V., Patel, M.K., Scanlan, C.N., Wormald, M.R., Finn, M.G., Burton, D.R., Wilson, I.A., Davis, B.G.

Revision History 

• Version 1.0: 2011-01-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-01-24
  Changes: Structure summary
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations