4RNR

Crystal structure of broadly neutralizing anti-HIV antibody PGT130


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.758 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Two Classes of Broadly Neutralizing Antibodies within a Single Lineage Directed to the High-Mannose Patch of HIV Envelope.

Doores, K.J.Kong, L.Krumm, S.A.Le, K.M.Sok, D.Laserson, U.Garces, F.Poignard, P.Wilson, I.A.Burton, D.R.

(2015) J.Virol. 89: 1105-1118

  • DOI: 10.1128/JVI.02905-14

  • PubMed Abstract: 
  • The high-mannose patch of human immunodeficiency virus (HIV) envelope (Env) elicits broadly neutralizing antibodies (bnAbs) during natural infection relatively frequently, and consequently, this region has become a major target of vaccine design. How ...

    The high-mannose patch of human immunodeficiency virus (HIV) envelope (Env) elicits broadly neutralizing antibodies (bnAbs) during natural infection relatively frequently, and consequently, this region has become a major target of vaccine design. However, it has also become clear that antibody recognition of the region is complex due, at least in part, to variability in neighboring loops and glycans critical to the epitopes. bnAbs against this region have some shared features and some distinguishing features that are crucial to understand in order to design optimal immunogens that can induce different classes of bnAbs against this region. Here, we compare two branches of a single antibody lineage, in which all members recognize the high-mannose patch. One branch (prototype bnAb PGT128) has a 6-amino-acid insertion in CDRH2 that is crucial for broad neutralization. Antibodies in this branch appear to favor a glycan site at N332 on gp120, and somatic hypermutation is required to accommodate the neighboring V1 loop glycans and glycan heterogeneity. The other branch (prototype bnAb PGT130) lacks the CDRH2 insertion. Antibodies in this branch are noticeably effective at neutralizing viruses with an alternate N334 glycan site but are less able to accommodate glycan heterogeneity. We identify a new somatic variant within this branch that is predominantly dependent on N334. The crystal structure of PGT130 offers insight into differences from PGT128. We conclude that different immunogens may be required to elicit bnAbs that have the optimal characteristics of the two branches of the lineage described.


    Organizational Affiliation

    Department of Infectious Diseases, King's College London, Faculty of Life Sciences and Medicine, Guy's Hospital, London, United Kingdom katie.doores@kcl.ac.uk burton@scripps.edu.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA Harvard-MIT Division of Health Sciences and Technology, Cambridge, Massachusetts, USA.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, USA Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California, USA Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA.,Department of Infectious Diseases, King's College London, Faculty of Life Sciences and Medicine, Guy's Hospital, London, United Kingdom.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, USA Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California, USA.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, USA.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, USA Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California, USA katie.doores@kcl.ac.uk burton@scripps.edu.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, USA Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California, USA International AIDS Vaccine Initiative, New York, New York, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PGT130 Heavy Chain
A, C
233N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PGT130 Light Chain
B, D
216N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.758 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.244 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 67.021α = 90.00
b = 69.052β = 90.00
c = 272.236γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
HKL-2000data reduction
PHENIXrefinement
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-10-24 
  • Released Date: 2014-11-19 
  • Deposition Author(s): Kong, L., Wilson, I.A.

Revision History 

  • Version 1.0: 2014-11-19
    Type: Initial release
  • Version 1.1: 2015-01-28
    Type: Database references