4M1D

Crystal structure of anti-HIV-1 Fab 447-52D in complex with V3 cyclic peptide MN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

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This is version 1.1 of the entry. See complete history


Literature

Thermodynamic Signatures of the Antigen Binding Site of mAb 447-52D Targeting the Third Variable Region of HIV-1 gp120.

Killikelly, A.Zhang, H.T.Spurrier, B.Williams, C.Gorny, M.K.Zolla-Pazner, S.Kong, X.P.

(2013) Biochemistry 52: 6249-6257

  • DOI: https://doi.org/10.1021/bi400645e
  • Primary Citation of Related Structures:  
    4M1D

  • PubMed Abstract: 

    The third variable region (V3) of HIV-1 gp120 plays a key role in viral entry into host cells; thus, it is a potential target for vaccine design. Human monoclonal antibody (mAb) 447-52D is one of the most broadly and potently neutralizing anti-V3 mAbs. We further characterized the 447-52D epitope by determining a high-resolution crystal structure of the Fab fragment in complex with a cyclic V3 and interrogated the antigen-antibody interaction by a combination of site-specific mutagenesis, isothermal titration calorimetry (ITC) and neutralization assays. We found that 447-52D's neutralization capability is correlated with its binding affinity and at 25 °C the Gibbs free binding energy is composed of a large enthalpic component and a small favorable entropic component. The large enthalpic contribution is due to (i) an extensive hydrogen bond network, (ii) a π-cation sandwiching the V3 crown apex residue Arg(315), and (iii) a salt bridge between the 447-52D heavy chain residue Asp(H95) and Arg(315). Arg(315) is often harbored by clade B viruses; thus, our data explained why 447-52D preferentially neutralizes clade B viruses. Interrogation of the thermodynamic signatures of residues at the antigen binding interface gives key insights into their contributions in the antigen-antibody interaction.


  • Organizational Affiliation

    Departments of Biochemistry and Molecular Pharmacology and ‡Department of Pathology, New York University School of Medicine , New York, New York 10016, United States.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fab mAb 447-52D Light ChainA [auth L],
D [auth M]
216Homo sapiensMutation(s): 0 
UniProt
Find proteins for A2NUT2 (Homo sapiens)
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Go to UniProtKB:  A2NUT2
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UniProt GroupA2NUT2
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab mAb 447-52D Heavy ChainB [auth H],
E [auth I]
231Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclic V3 Arch PeptideC [auth P],
F [auth Q]
14Human immunodeficiency virus type 1 group M subtype B (isolate MN)Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for P05877 (Human immunodeficiency virus type 1 group M subtype B (isolate MN))
Explore P05877 
Go to UniProtKB:  P05877
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UniProt GroupP05877
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth L]
H [auth L]
I [auth L]
J [auth L]
K [auth L]
G [auth L],
H [auth L],
I [auth L],
J [auth L],
K [auth L],
L,
M [auth H],
N [auth H],
O [auth H],
P [auth H],
Q [auth H],
R [auth H],
S [auth M],
T [auth M],
U [auth M],
V [auth I],
W [auth I]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 179.836α = 90
b = 59.781β = 127.35
c = 137.066γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-04
    Type: Initial release
  • Version 1.1: 2013-12-25
    Changes: Database references