Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A1BCDEF Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A2BC1D 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 177.37 kDa 
• Atom Count: 11946 
• Residue Count: 1473 
• Unique protein chains: 6

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

• DOI: 10.2210/pdb6CE0/pdb

• Classification: viral protein/immune system
• Organism(s): Human immunodeficiency virus 1, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2018-02-09 Released: 2018-12-05 
• Deposition Author(s): Kumar, S., Sarkar, A., Wilson, I.A.

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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 

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

• PubMed: 30474059 
• 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 ) 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Envelope glycoprotein gp160	G	487	Human immunodeficiency virus 1	Mutation(s): 1  Gene Names: env
Find proteins for A4ZPX1 (Human immunodeficiency virus 1) Go to UniProtKB:  A4ZPX1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
35O22 Heavy chain	D	243	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
35O22 Light chain	E	216	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
PGT124 Heavy chain	H	236	Homo sapiens	Mutation(s): 0

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Envelope glycoprotein gp160	B	140	Human immunodeficiency virus 1	Mutation(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

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details
PGT124 Light chain	L	214	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B, D, G, H	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
BMA	D, G, H	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
MAN	D, G, H	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N

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 = 127.351	α = 90
b = 127.351	β = 90
c = 316.35	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-02-09 
• Released Date: 2018-12-05 
Deposition Author(s): Kumar, S., Sarkar, A., Wilson, I.A.

Revision History 

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