5JSA

Uncleaved prefusion optimized gp140 trimer with an engineered 10-residue HR1 turn bound to broadly neutralizing antibodies 8ANC195 and PGT128

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.308 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.281 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Uncleaved prefusion-optimized gp140 trimers derived from analysis of HIV-1 envelope metastability.

Kong, L., He, L., de Val, N., Vora, N., Morris, C.D., Azadnia, P., Sok, D., Zhou, B., Burton, D.R., Ward, A.B., Wilson, I.A., Zhu, J.

(2016) Nat Commun 7: 12040-12040

  • DOI: 10.1038/ncomms12040
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The trimeric HIV-1 envelope glycoprotein (Env) is critical for host immune recognition and neutralization. Despite advances in trimer design, the roots of Env trimer metastability remain elusive. Here we investigate the contribution of two Env region ...

    The trimeric HIV-1 envelope glycoprotein (Env) is critical for host immune recognition and neutralization. Despite advances in trimer design, the roots of Env trimer metastability remain elusive. Here we investigate the contribution of two Env regions to metastability. First, we computationally redesign a largely disordered bend in heptad region 1 (HR1) of SOSIP trimers that connects the long, central HR1 helix to the fusion peptide, substantially improving the yield of soluble, well-folded trimers. Structural and antigenic analyses of two distinct HR1 redesigns confirm that redesigned Env closely mimics the native, prefusion trimer with a more stable gp41. Next, we replace the cleavage site between gp120 and gp41 with various linkers in the context of an HR1 redesign. Electron microscopy reveals a potential fusion intermediate state for uncleaved trimers containing short but not long linkers. Together, these results outline a general approach for stabilization of Env trimers from diverse HIV-1 strains.

    Organizational Affiliation: 

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
broadly neutralizing antibody PGT128 heavy chain
A
239N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
broadly neutralizing antibody PGT128 light chain
B
211N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
gp120
C
480Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q2N0S6
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
gp41
D
142Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q2N0S6
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
broadly neutralizing antibody 8ANC195 heavy chain
E
238N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
broadly neutralizing antibody 8ANC195 light chain
F
215N/AMutation(s): 0 
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 
C, D, E
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA
Download SDF File 
Download CCD File 
C, D, E
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
Download CCD File 
C, D, E
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.308 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.281 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 266.279α = 90.00
b = 266.279β = 90.00
c = 266.279γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2016-05-07 
  • Released Date: 2016-07-13 
  • Deposition Author(s): Kong, L., Wilson, I.A.

Revision History 

  • Version 1.0: 2016-07-13
    Type: Initial release
  • Version 1.1: 2018-03-21
    Type: Advisory, Derived calculations