5O2U

Llama VHH in complex with p24


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Unravelling the Molecular Basis of High Affinity Nanobodies against HIV p24: In Vitro Functional, Structural, and in Silico Insights.

Gray, E.R.Brookes, J.C.Caillat, C.Turbe, V.Webb, B.L.J.Granger, L.A.Miller, B.S.McCoy, L.E.El Khattabi, M.Verrips, C.T.Weiss, R.A.Duffy, D.M.Weissenhorn, W.McKendry, R.A.

(2017) ACS Infect Dis 3: 479-491

  • DOI: 10.1021/acsinfecdis.6b00189

  • PubMed Abstract: 
  • Preventing the spread of infectious diseases remains an urgent priority worldwide, and this is driving the development of advanced nanotechnology to diagnose infections at the point of care. Herein, we report the creation of a library of novel nanobo ...

    Preventing the spread of infectious diseases remains an urgent priority worldwide, and this is driving the development of advanced nanotechnology to diagnose infections at the point of care. Herein, we report the creation of a library of novel nanobody capture ligands to detect p24, one of the earliest markers of HIV infection. We demonstrate that these nanobodies, one tenth the size of conventional antibodies, exhibit high sensitivity and broad specificity to global HIV-1 subtypes. Biophysical characterization indicates strong 690 pM binding constants and fast kinetic on-rates, 1 to 2 orders of magnitude better than monoclonal antibody comparators. A crystal structure of the lead nanobody and p24 was obtained and used alongside molecular dynamics simulations to elucidate the molecular basis of these enhanced performance characteristics. They indicate that binding occurs at C-terminal helices 10 and 11 of p24, a negatively charged region of p24 complemented by the positive surface of the nanobody binding interface involving CDR1, CDR2, and CDR3 loops. Our findings have broad implications on the design of novel antibodies and a wide range of advanced biomedical applications.


    Organizational Affiliation

    QVQ Holding B.V. , Yalelaan 1, 3584CL, Utrecht, The Netherlands.,London Centre for Nanotechnology, Division of Medicine and Department of Physics and Astronomy, University College London , 17-19 Gordon Street, London, WC1H 0AH, United Kingdom.,Univ. Grenoble Alpes, CEA, CNRS, IBS , 71 Avenue des Martyrs, Grenoble, 38000, France.,Division of Infection and Immunity, University College London , The Cruciform Building, Gower Street, London, WC1E 6BT, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsid protein p24
A, C
500Human immunodeficiency virus type 1 group M subtype B (isolate NY5)Mutation(s): 0 
Gene Names: gag
Find proteins for P12493 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Go to UniProtKB:  P12493
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
VHH 59H10
B, D
132N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.222 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 40.993α = 90.00
b = 72.228β = 91.40
c = 69.953γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-06-21
    Type: Initial release
  • Version 1.1: 2017-07-26
    Type: Database references