Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - ABC Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer -A2B 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 89023.03 
• Atom Count: 6146 
• Residue Count: 785 
• Unique protein chains: 3

5TE7

Crystal Structure of Broadly Neutralizing VRC01-class Antibody N6 in Complex with HIV-1 Clade C Strain DU172.17 gp120 Core

• DOI: 10.2210/pdb5TE7/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Human immunodeficiency virus 1
• Expression System: Homo sapiens


• Deposited: 2016-09-20 Released: 2016-11-16 
• Deposition Author(s): Zhou, T., Kwong, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.228 
• R-Value Work: 0.190 

Literature

Identification of a CD4-Binding-Site Antibody to HIV that Evolved Near-Pan Neutralization Breadth.

Huang, J., Kang, B.H., Ishida, E., Zhou, T., Griesman, T., Sheng, Z., Wu, F., Doria-Rose, N.A., Zhang, B., McKee, K., O'Dell, S., Chuang, G.Y., Druz, A., Georgiev, I.S., Schramm, C.A., Zheng, A., Joyce, M.G., Asokan, M., Ransier, A., Darko, S., Migueles, S.A., Bailer, R.T., Louder, M.K., Alam, S.M., Parks, R., Kelsoe, G., Von Holle, T., Haynes, B.F., Douek, D.C., Hirsch, V., Seaman, M.S., Shapiro, L., Mascola, J.R., Kwong, P.D., Connors, M.

(2016) Immunity 45: 1108-1121

• PubMed: 27851912 
• DOI: 10.1016/j.immuni.2016.10.027
• Primary Citation of Related Structures:  
  5TE6, 5TE4


• PubMed Abstract: 
  

Detailed studies of the broadly neutralizing antibodies (bNAbs) that underlie the best available examples of the humoral immune response to HIV are providing important information for the development of therapies and prophylaxis for HIV-1 infection. Here, we report a CD4-binding site (CD4bs) antibody, named N6, that potently neutralized 98% of HIV-1 isolates, including 16 of 20 that were resistant to other members of its class. N6 evolved a mode of recognition such that its binding was not impacted by the loss of individual contacts across the immunoglobulin heavy chain. In addition, structural analysis revealed that the orientation of N6 permitted it to avoid steric clashes with glycans, which is a common mechanism of resistance. Thus, an HIV-1-specific bNAb can achieve potent, near-pan neutralization of HIV-1, making it an attractive candidate for use in therapy and prophylaxis.

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Organizational Affiliation: 

HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Heavy chain of N6	H	225	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Light chain of N6	L	210	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
HIV-1 gp120 core	G	350	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: env
Find proteins for Q202J8 (Human immunodeficiency virus 1) Go to UniProtKB:  Q202J8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
EPE	G, H	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HEPES C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
EDO	G, H, L	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NAG	G, L	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.228 
• R-Value Work: 0.190 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 62.675	α = 90.00
b = 65.547	β = 90.00
c = 241.522	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-09-20 
• Released Date: 2016-11-16 
• Deposition Author(s): Zhou, T., Kwong, P.D.

Revision History 

• Version 1.0: 2016-11-16
  Type: Initial release
• Version 1.1: 2016-11-23
  Type: Database references, Structure summary
• Version 1.2: 2016-11-30
  Type: Database references