5TE7

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 


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

  • DOI: 10.1016/j.immuni.2016.10.027
  • Structures With Same Primary Citation

  • 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. ...

    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.

    Organizational Affiliation: 

    HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA. Electronic address: mconnors@nih.gov.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Heavy chain of N6H225Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Light chain of N6L210Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HIV-1 gp120 coreG350Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Find proteins for Q202J8 (Human immunodeficiency virus 1)
Explore Q202J8 
Go to UniProtKB:  Q202J8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE
Download CCD File 
G, H
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N		 Ligand Interaction
NAG
Query on NAG
Download CCD File 
G, L
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
EDO
Query on EDO
Download CCD File 
G, H, L
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.675α = 90
b = 65.547β = 90
c = 241.522γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
Cootmodel building

Structure Validation

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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
    Changes: Database references, Structure summary
  • Version 1.2: 2016-11-30
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary