4YAQ

Crystal structure of a computationally optimized PG9 mutant

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Redesigned HIV antibodies exhibit enhanced neutralizing potency and breadth.

Willis, J.R., Sapparapu, G., Murrell, S., Julien, J.P., Singh, V., King, H.G., Xia, Y., Pickens, J.A., LaBranche, C.C., Slaughter, J.C., Montefiori, D.C., Wilson, I.A., Meiler, J., Crowe, J.E.

(2015) J.Clin.Invest. 125: 2523-2531

  • DOI: 10.1172/JCI80693

  • PubMed Abstract: 

    • Several HIV envelope-targeting (Env-targeting) antibodies with broad and potent neutralizing activity have been identified and shown to have unusual features. Of these, the PG9 antibody has a long heavy chain complementarity determining region 3 (HCD ...

    Several HIV envelope-targeting (Env-targeting) antibodies with broad and potent neutralizing activity have been identified and shown to have unusual features. Of these, the PG9 antibody has a long heavy chain complementarity determining region 3 (HCDR3) and possesses unique structural elements that interact with protein and glycan features of the HIV Env glycoprotein. Here, we used the Rosetta software suite to design variants of the PG9 antibody HCDR3 loop with the goal of identifying variants with increased potency and breadth of neutralization for diverse HIV strains. One variant, designated PG9_N100(F)Y, possessed increased potency and was able to neutralize a diverse set of PG9-resistant HIV strains, including those lacking the Env N160 glycan, which is critical for PG9 binding. An atomic resolution structure of the PG9_N100(F)Y fragment antigen binding (Fab) confirmed that the mutated residue retains the paratope surface when compared with WT PG9. Differential scanning calorimetry experiments revealed that the mutation caused a modest increase in thermodynamic stability of the Fab, a feature predicted by the computational model. Our findings suggest that thermodynamic stabilization of the long HCDR3 in its active conformation is responsible for the increased potency of PG9_N100(F)Y, and strategies aimed at stabilizing this region in other HIV antibodies could become an important approach to in silico optimization of antibodies.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PG9_N100FY Fab heavy chain
H, A
248N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PG9_N100FY Light Chain
L, B
216Homo sapiensMutation(s): 0 
Gene Names: IGL@
Find proteins for Q6GMW3 (Homo sapiens)
Go to UniProtKB:  Q6GMW3
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4
Download SDF File 
Download CCD File 
H, L
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
FUC
Query on FUC
Download SDF File 
Download CCD File 
B, L
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
Download CCD File 
B, L
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
MES
Query on MES
Download SDF File 
Download CCD File 
B, H, L
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A, H
L-PEPTIDE LINKINGC5 H7 N O3GLU
TYS
Query on TYS
A, H
L-PEPTIDE LINKINGC9 H11 N O6 STYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 57.740α = 90.00
b = 122.980β = 96.27
c = 69.920γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-06-03
    Type: Initial release
  • Version 1.1: 2015-06-10
    Type: Database references
  • Version 1.2: 2017-08-23
    Type: Author supporting evidence, Database references, Derived calculations, Source and taxonomy