5TE7 | pdb_00005te7

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 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5TE7

Ligand Structure Quality Assessment 


This is version 1.5 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: https://doi.org/10.1016/j.immuni.2016.10.027
  • Primary Citation Related Structures: 
    5TE4, 5TE6, 5TE7

  • 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.


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

Macromolecule Content 

  • Total Structure Weight: 89.02 kDa 
  • Atom Count: 6,461 
  • Modeled Residue Count: 771 
  • Deposited Residue Count: 785 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Heavy chain of N6A [auth H]225Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Light chain of N6B [auth L]210Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
HIV-1 gp120 coreC [auth G]350Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for Q202J8 (Human immunodeficiency virus type 1)
Explore Q202J8 
Go to UniProtKB:  Q202J8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ202J8
Glycosylation
Glycosylation Sites: 7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE

Query on EPE



Download:Ideal Coordinates CCD File
D [auth H],
R [auth G]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
G [auth L]
K [auth G]
L [auth G]
M [auth G]
N [auth G]
G [auth L],
K [auth G],
L [auth G],
M [auth G],
N [auth G],
O [auth G],
P [auth G],
Q [auth G]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
E [auth H]
F [auth H]
H [auth L]
I [auth L]
J [auth L]
E [auth H],
F [auth H],
H [auth L],
I [auth L],
J [auth L],
S [auth G],
T [auth G]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.228 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
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

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.5: 2024-11-06
    Changes: Structure summary