5I8H

Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer in Complex with V3 Loop-targeting Antibody PGT122 Fab and Fusion Peptide-targeting Antibody VRC34.01 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.301 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.281 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Fusion peptide of HIV-1 as a site of vulnerability to neutralizing antibody.

Kong, R.Xu, K.Zhou, T.Acharya, P.Lemmin, T.Liu, K.Ozorowski, G.Soto, C.Taft, J.D.Bailer, R.T.Cale, E.M.Chen, L.Choi, C.W.Chuang, G.Y.Doria-Rose, N.A.Druz, A.Georgiev, I.S.Gorman, J.Huang, J.Joyce, M.G.Louder, M.K.Ma, X.McKee, K.O'Dell, S.Pancera, M.Yang, Y.Blanchard, S.C.Mothes, W.Burton, D.R.Koff, W.C.Connors, M.Ward, A.B.Kwong, P.D.Mascola, J.R.

(2016) Science 352: 828-833

  • DOI: 10.1126/science.aae0474
  • Primary Citation of Related Structures:  5I8C, 5I8E

  • PubMed Abstract: 
  • The HIV-1 fusion peptide, comprising 15 to 20 hydrophobic residues at the N terminus of the Env-gp41 subunit, is a critical component of the virus-cell entry machinery. Here, we report the identification of a neutralizing antibody, N123-VRC34.01, whi ...

    The HIV-1 fusion peptide, comprising 15 to 20 hydrophobic residues at the N terminus of the Env-gp41 subunit, is a critical component of the virus-cell entry machinery. Here, we report the identification of a neutralizing antibody, N123-VRC34.01, which targets the fusion peptide and blocks viral entry by inhibiting conformational changes in gp120 and gp41 subunits of Env required for entry. Crystal structures of N123-VRC34.01 liganded to the fusion peptide, and to the full Env trimer, revealed an epitope consisting of the N-terminal eight residues of the gp41 fusion peptide and glycan N88 of gp120, and molecular dynamics showed that the N-terminal portion of the fusion peptide can be solvent-exposed. These results reveal the fusion peptide to be a neutralizing antibody epitope and thus a target for vaccine design.


    Organizational Affiliation

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BG505 SOSIP.664 gp120
A, C
481Human immunodeficiency virus 1Gene Names: env
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q2N0S6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BG505 SOSIP.664 gp41
B, D
153Human immunodeficiency virus 1Gene Names: env
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q2N0S6
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PGT122 Fab light chain
L, J
210N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
VRC34.01 Fab heavy chain
E, G
223N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
VRC34.01 Fab light chain
F, H
212N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
PGT122 Fab heavy chain
I, K
235N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, C, I
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, C, I
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D, I, K
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.301 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.281 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 252.296α = 90.00
b = 252.296β = 90.00
c = 561.202γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data collection
PHASERphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of HealthUnited StatesIntramural

Revision History 

  • Version 1.0: 2016-05-25
    Type: Initial release
  • Version 1.1: 2016-06-01
    Type: Derived calculations
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Derived calculations