4DQO

Crystal Structure of PG16 Fab in Complex with V1V2 Region from HIV-1 strain ZM109


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.438 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis for diverse N-glycan recognition by HIV-1-neutralizing V1-V2-directed antibody PG16.

Pancera, M.Shahzad-Ul-Hussan, S.Doria-Rose, N.A.McLellan, J.S.Bailer, R.T.Dai, K.Loesgen, S.Louder, M.K.Staupe, R.P.Yang, Y.Zhang, B.Parks, R.Eudailey, J.Lloyd, K.E.Blinn, J.Alam, S.M.Haynes, B.F.Amin, M.N.Wang, L.X.Burton, D.R.Koff, W.C.Nabel, G.J.Mascola, J.R.Bewley, C.A.Kwong, P.D.

(2013) Nat.Struct.Mol.Biol. 20: 804-813

  • DOI: 10.1038/nsmb.2600

  • PubMed Abstract: 
  • HIV-1 uses a diverse N-linked-glycan shield to evade recognition by antibody. Select human antibodies, such as the clonally related PG9 and PG16, recognize glycopeptide epitopes in the HIV-1 V1-V2 region and penetrate this shield, but their ability t ...

    HIV-1 uses a diverse N-linked-glycan shield to evade recognition by antibody. Select human antibodies, such as the clonally related PG9 and PG16, recognize glycopeptide epitopes in the HIV-1 V1-V2 region and penetrate this shield, but their ability to accommodate diverse glycans is unclear. Here we report the structure of antibody PG16 bound to a scaffolded V1-V2, showing an epitope comprising both high mannose-type and complex-type N-linked glycans. We combined structure, NMR and mutagenesis analyses to characterize glycan recognition by PG9 and PG16. Three PG16-specific residues, arginine, serine and histidine (RSH), were critical for binding sialic acid on complex-type glycans, and introduction of these residues into PG9 produced a chimeric antibody with enhanced HIV-1 neutralization. Although HIV-1-glycan diversity facilitates evasion, antibody somatic diversity can overcome this and can provide clues to guide the design of modified antibodies with enhanced neutralization.


    Organizational Affiliation

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PG16 Fab Heavy Chain
H
246N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PG16 Fab Light Chain
L
216N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
1FD6-V1V2 scaffold ZM109 HIV-1 strain
C
124Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Find proteins for Q6TCP8 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q6TCP8
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
C
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
GAL
Query on GAL

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Download CCD File 
C
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
C
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
C
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
SIA
Query on SIA

Download SDF File 
Download CCD File 
C
O-SIALIC ACID
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
H
L-PEPTIDE LINKINGC5 H7 N O3GLU
TYS
Query on TYS
H
L-PEPTIDE LINKINGC9 H11 N O6 STYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.438 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.201 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 81.054α = 90.00
b = 207.561β = 90.00
c = 87.617γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-06
    Type: Initial release
  • Version 1.1: 2013-05-08
    Type: Derived calculations, Other
  • Version 1.2: 2013-06-05
    Type: Database references
  • Version 1.3: 2013-07-24
    Type: Database references