6CE0

Crystal structure of a HIV-1 clade B tier-3 isolate H078.14 UFO-BG Env trimer in complex with broadly neutralizing Fabs PGT124 and 35O22 at 4.6 Angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.60 Å
  • R-Value Free: 0.341 
  • R-Value Work: 0.313 
  • R-Value Observed: 0.314 

wwPDB Validation 3D Report Full Report



Literature

HIV-1 vaccine design through minimizing envelope metastability.

He, L.Kumar, S.Allen, J.D.Huang, D.Lin, X.Mann, C.J.Saye-Francisco, K.L.Copps, J.Sarkar, A.Blizard, G.S.Ozorowski, G.Sok, D.Crispin, M.Ward, A.B.Nemazee, D.Burton, D.R.Wilson, I.A.Zhu, J.

(2018) Sci Adv 4: eaau6769-eaau6769

  • DOI: 10.1126/sciadv.aau6769
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Overcoming envelope metastability is crucial to trimer-based HIV-1 vaccine design. Here, we present a coherent vaccine strategy by minimizing metastability. For 10 strains across five clades, we demonstrate that the gp41 ectodomain (gp41 ECTO

    Overcoming envelope metastability is crucial to trimer-based HIV-1 vaccine design. Here, we present a coherent vaccine strategy by minimizing metastability. For 10 strains across five clades, we demonstrate that the gp41 ectodomain (gp41 ECTO ) is the main source of envelope metastability by replacing wild-type gp41 ECTO with BG505 gp41 ECTO of the uncleaved prefusion-optimized (UFO) design. These gp41 ECTO -swapped trimers can be produced in CHO cells with high yield and high purity. The crystal structure of a gp41 ECTO -swapped trimer elucidates how a neutralization-resistant tier 3 virus evades antibody recognition of the V2 apex. UFO trimers of transmitted/founder viruses and UFO trimers containing a consensus-based ancestral gp41 ECTO suggest an evolutionary root of metastability. The gp41 ECTO -stabilized trimers can be readily displayed on 24- and 60-meric nanoparticles, with incorporation of additional T cell help illustrated for a hyperstable 60-mer, I3-01. In mice and rabbits, these gp140 nanoparticles induced tier 2 neutralizing antibody responses more effectively than soluble trimers.


    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp160
G
487Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: env
Find proteins for A4ZPX1 (Human immunodeficiency virus 1)
Go to UniProtKB:  A4ZPX1
Protein Feature View
  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
35O22 Heavy chain
D
243Homo sapiensMutation(s): 0 
Protein Feature View
  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
35O22 Light chain
E
216Homo sapiensMutation(s): 0 
Protein Feature View
  • Reference Sequence

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
PGT124 Heavy chain
H
236Homo sapiensMutation(s): 0 
Protein Feature View
  • Reference Sequence

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp160
B
140Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: env
Find proteins for Q2N0S5 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q2N0S5
Find proteins for Q2N0T3 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q2N0T3
Protein Feature View
  • Reference Sequence

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
PGT124 Light chain
L
214Homo sapiensMutation(s): 0 
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
B, D, G, H
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
BMA
Query on BMA

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D, G, H
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
MAN
Query on MAN

Download CCD File 
D, G, H
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.60 Å
  • R-Value Free: 0.341 
  • R-Value Work: 0.313 
  • R-Value Observed: 0.314 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.351α = 90
b = 127.351β = 90
c = 316.35γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-12-05
    Type: Initial release