Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1BC 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 58.02 kDa 
• Atom Count: 4662 
• Residue Count: 523 
• Unique protein chains: 3

4AL8

Structure of Dengue virus DIII in complex with Fab 2H12

• DOI: 10.2210/pdb4AL8/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Dengue virus, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-03-02 Released: 2012-06-06 
• Deposition Author(s): Midgley, C.M., Flanagan, A., Mongkolsapaya, J., Grimes, J.M., Screaton, G.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 0.198 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 

Literature

Structural Analysis of a Dengue Cross-Reactive Antibody Complexed with Envelope Domain III Reveals the Molecular Basis of Cross-Reactivity.

Midgley, C.M., Flanagan, A., Tran, H.B., Dejnirattisai, W., Chawansuntati, K., Jumnainsong, A., Wongwiwat, W., Duangchinda, T., Mongkolsapaya, J., Grimes, J.M., Screaton, G.R.

(2012) J Immunol 188: 4971

• PubMed: 22491255 
• DOI: 10.4049/jimmunol.1200227
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Dengue virus infections are still increasing at an alarming rate in tropical and subtropical countries, underlying the need for a dengue vaccine. Although it is relatively easy to generate Ab responses to dengue virus, low avidity or low concentrations of Ab may enhance infection of FcR-bearing cells with clinical impact, posing a challenge to vaccine production. In this article, we report the characterization of a mAb, 2H12, which is cross-reactive to all four serotypes in the dengue virus group. Crystal structures of 2H12-Fab in complex with domain III of the envelope protein from three dengue serotypes have been determined. 2H12 binds to the highly conserved AB loop of domain III of the envelope protein that is poorly accessible in the mature virion. 2H12 neutralization varied between dengue serotypes and strains; in particular, dengue serotype 2 was not neutralized. Because the 2H12-binding epitope was conserved, this variation in neutralization highlights differences between dengue serotypes and suggests that significant conformational changes in the virus must take place for Ab binding. Surprisingly, 2H12 facilitated little or no enhancement of infection. These data provide a structural basis for understanding Ab neutralization and enhancement of infection, which is crucial for the development of future dengue vaccines.

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Organizational Affiliation: 

Department of Medicine, Hammersmith Hospital Campus, Imperial College London, London W12 0NN, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
ENVELOPE PROTEIN	C	101	Dengue virus	Mutation(s): 0  EC: 3.4.21.91 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.1.1.56 (UniProt), 2.1.1.57 (UniProt), 2.7.7.48 (UniProt)
Find proteins for P17763 (Dengue virus type 1 (strain Nauru/West Pac/1974)) Explore P17763  Go to UniProtKB:  P17763

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
FAB 2H12 HEAVY CHAIN	H	217	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
FAB 2H12 LIGHT CHAIN	L	213	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	H, L	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 0.198 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.401	α = 93.32
b = 60.603	β = 102.1
c = 62.833	γ = 101.51

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-03-02 
• Released Date: 2012-06-06 
Deposition Author(s): Midgley, C.M., Flanagan, A., Mongkolsapaya, J., Grimes, J.M., Screaton, G.R.

Revision History 

• Version 1.0: 2012-06-06
  Type: Initial release