5UY3

Crystal structure of human Fab PGT144, a broadly reactive and potent HIV-1 neutralizing antibody

  • Classification: IMMUNE SYSTEM
  • Expression System: Homo sapiens

  • Deposited: 2017-02-23 Released: 2017-04-19 
  • Deposition Author(s): Julien, J.-P., Lee, J.H., Wilson, I.A.
  • Funding Organization(s): California HIV/AIDS Research Program Dissertation Award; Scripps CHAVI-ID; National Institutes of Health/National Institute Of Allergy and Infectious Diseases; International AIDS Vaccine Initiative; Bill & Melinda Gates Foundation 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.241 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Broadly Neutralizing Antibody Targets the Dynamic HIV Envelope Trimer Apex via a Long, Rigidified, and Anionic beta-Hairpin Structure.

Lee, J.H.Andrabi, R.Su, C.Y.Yasmeen, A.Julien, J.P.Kong, L.Wu, N.C.McBride, R.Sok, D.Pauthner, M.Cottrell, C.A.Nieusma, T.Blattner, C.Paulson, J.C.Klasse, P.J.Wilson, I.A.Burton, D.R.Ward, A.B.

(2017) Immunity 46: 690-702

  • DOI: 10.1016/j.immuni.2017.03.017
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Broadly neutralizing antibodies (bnAbs) to HIV delineate vaccine targets and are prophylactic and therapeutic agents. Some of the most potent bnAbs target a quaternary epitope at the apex of the surface HIV envelope (Env) trimer. Using cryo-electron ...

    Broadly neutralizing antibodies (bnAbs) to HIV delineate vaccine targets and are prophylactic and therapeutic agents. Some of the most potent bnAbs target a quaternary epitope at the apex of the surface HIV envelope (Env) trimer. Using cryo-electron microscopy, we solved the atomic structure of an apex bnAb, PGT145, in complex with Env. We showed that the long anionic HCDR3 of PGT145 penetrated between glycans at the trimer 3-fold axis, to contact peptide residues from all three Env protomers, and thus explains its highly trimer-specific nature. Somatic hypermutation in the other CDRs of PGT145 were crucially involved in stabilizing the structure of the HCDR3, similar to bovine antibodies, to aid in recognition of a cluster of conserved basic residues hypothesized to facilitate trimer disassembly during viral entry. Overall, the findings exemplify the creative solutions that the human immune system can evolve to recognize a conserved motif buried under a canopy of glycans.


    Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, International AIDS Vaccine Initiative Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Antibody PGT144 Fab light chain
L, B
216N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Antibody PGT144 Fab heavy chain
H, A
238N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS
A, H
L-PEPTIDE LINKINGC9 H11 N O6 STYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.241 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 57.600α = 82.04
b = 67.550β = 74.89
c = 69.550γ = 81.26
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
California HIV/AIDS Research Program Dissertation AwardUnited StatesD12-SRI-353
Scripps CHAVI-IDUnited StatesUM1 AI100663
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI110657
International AIDS Vaccine InitiativeUnited States--
Bill & Melinda Gates FoundationUnited StatesOPP1115782 and OPP1084519

Revision History 

  • Version 1.0: 2017-04-19
    Type: Initial release
  • Version 1.1: 2017-05-03
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Author supporting evidence