Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 99.86 kDa 
• Atom Count: 8039 
• Residue Count: 919 
• Unique protein chains: 3

4M1D

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

• DOI: 10.2210/pdb4M1D/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2013-08-02 Released: 2013-09-04 
• Deposition Author(s): Killikelly, A., Kong, X.P.

---

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 

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

• PubMed: 23944979 
• DOI: 10.1021/bi400645e
• Structures With Same Primary Citation


• 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Fab mAb 447-52D Light Chain	L, M	216	Homo sapiens	Mutation(s): 0
Find proteins for A2NUT2 (Homo sapiens) Explore A2NUT2  Go to UniProtKB:  A2NUT2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Fab mAb 447-52D Heavy Chain	H, I	231	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Cyclic V3 Arch Peptide	P, Q	14	N/A	Mutation(s): 0
Find proteins for P05877 (Human immunodeficiency virus type 1 group M subtype B (isolate MN)) Explore P05877  Go to UniProtKB:  P05877

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	H, I, L, M	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 = 179.836	α = 90
b = 59.781	β = 127.35
c = 137.066	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-08-02 
• Released Date: 2013-09-04 
Deposition Author(s): Killikelly, A., Kong, X.P.

Revision History 

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