5ESV

Crystal Structure of Broadly Neutralizing Antibody CH03, Isolated from Donor CH0219, in Complex with Scaffolded Trimeric HIV-1 Env V1V2 Domain from the Clade C Superinfecting Strain of Donor CAP256.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.105 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of HIV-1 Env V1V2 with broadly neutralizing antibodies reveal commonalities that enable vaccine design.

Gorman, J.Soto, C.Yang, M.M.Davenport, T.M.Guttman, M.Bailer, R.T.Chambers, M.Chuang, G.Y.DeKosky, B.J.Doria-Rose, N.A.Druz, A.Ernandes, M.J.Georgiev, I.S.Jarosinski, M.C.Joyce, M.G.Lemmin, T.M.Leung, S.Louder, M.K.McDaniel, J.R.Narpala, S.Pancera, M.Stuckey, J.Wu, X.Yang, Y.Zhang, B.Zhou, T.Program, N.C.Mullikin, J.C.Baxa, U.Georgiou, G.McDermott, A.B.Bonsignori, M.Haynes, B.F.Moore, P.L.Morris, L.Lee, K.K.Shapiro, L.Mascola, J.R.Kwong, P.D.

(2016) Nat.Struct.Mol.Biol. 23: 81-90

  • DOI: 10.1038/nsmb.3144
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Broadly neutralizing antibodies (bNAbs) against HIV-1 Env V1V2 arise in multiple donors. However, atomic-level interactions had previously been determined only with antibodies from a single donor, thus making commonalities in recognition uncertain. H ...

    Broadly neutralizing antibodies (bNAbs) against HIV-1 Env V1V2 arise in multiple donors. However, atomic-level interactions had previously been determined only with antibodies from a single donor, thus making commonalities in recognition uncertain. Here we report the cocrystal structure of V1V2 with antibody CH03 from a second donor and model Env interactions of antibody CAP256-VRC26 from a third donor. These V1V2-directed bNAbs used strand-strand interactions between a protruding antibody loop and a V1V2 strand but differed in their N-glycan recognition. Ontogeny analysis indicated that protruding loops develop early, and glycan interactions mature over time. Altogether, the multidonor information suggested that V1V2-directed bNAbs form an 'extended class', for which we engineered ontogeny-specific antigens: Env trimers with chimeric V1V2s that interacted with inferred ancestor and intermediate antibodies. The ontogeny-based design of vaccine antigens described here may provide a general means for eliciting antibodies of a desired class.


    Organizational Affiliation

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, Maryland, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CH03 Heavy Chain
A, C, H
244N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CH03 Light Chain
B, D, L
215N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase,Envelope glycoprotein gp160
E, F, G
211Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)Human immunodeficiency virus 1
This entity is chimeric
Mutation(s): 0 
Gene Names: ispF, env
EC: 4.6.1.12
Find proteins for P44815 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Go to UniProtKB:  P44815
Find proteins for W6ICC0 (Human immunodeficiency virus 1)
Go to UniProtKB:  W6ICC0
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
E, F, G
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
E, F, G
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
E, F, G
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
E, F, G
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.105 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.208 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 162.693α = 90.00
b = 98.211β = 112.82
c = 170.629γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-16
    Type: Initial release
  • Version 1.1: 2016-01-06
    Type: Database references
  • Version 1.2: 2016-01-13
    Type: Database references