6CE0 | pdb_00006ce0

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 (Depositor), 0.345 (DCC) 
  • R-Value Work: 
    0.313 (Depositor), 0.314 (DCC) 
  • R-Value Observed: 
    0.314 (Depositor) 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 3.0 of the entry. See complete history

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: https://doi.org/10.1126/sciadv.aau6769
  • Primary Citation Related Structures: 
    6CE0

  • 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.


  • Organizational Affiliation
    • Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.

Macromolecule Content 

  • Total Structure Weight: 176.94 kDa 
  • Atom Count: 11,946 
  • Modeled Residue Count: 1,473 
  • Deposited Residue Count: 1,536 
  • Unique protein chains: 6

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp160A [auth B]140Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: env
UniProt
Find proteins for Q2N0S5 (Human immunodeficiency virus type 1)
Explore Q2N0S5 
Go to UniProtKB:  Q2N0S5
Find proteins for Q2N0T3 (Human immunodeficiency virus type 1)
Explore Q2N0T3 
Go to UniProtKB:  Q2N0T3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ2N0T3Q2N0S5
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp160B [auth G]487Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: env
UniProt
Find proteins for A4ZPX1 (Human immunodeficiency virus type 1)
Explore A4ZPX1 
Go to UniProtKB:  A4ZPX1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4ZPX1
Glycosylation
Glycosylation Sites: 21
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
35O22 Heavy chainC [auth D]243Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
35O22 Light chainD [auth E]216Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
PGT124 Heavy chainE [auth H]236Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
PGT124 Light chainF [auth L]214Homo sapiensMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 7
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth A],
H [auth C],
K [auth J]
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 8
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseI [auth F],
L [auth K]
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 9
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseJ [auth I],
N
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO
GlyCosmos: G22768VO
GlyGen: G22768VO
Entity ID: 10
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
M
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD
GlyCosmos: G81315DD
GlyGen: G81315DD
Entity ID: 11
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
O
7N-Glycosylation
Glycosylation Resources
GlyTouCan: G07617FP
GlyCosmos: G07617FP
GlyGen: G07617FP

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
AA [auth G]
BA [auth G]
P [auth G]
Q [auth G]
R [auth G]
AA [auth G],
BA [auth G],
P [auth G],
Q [auth G],
R [auth G],
S [auth G],
T [auth G],
U [auth G],
V [auth G],
W [auth G],
X [auth G],
Y [auth G],
Z [auth G]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.60 Å
  • R-Value Free:  0.341 (Depositor), 0.345 (DCC) 
  • R-Value Work:  0.313 (Depositor), 0.314 (DCC) 
  • R-Value Observed: 0.314 (Depositor) 
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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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-05
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 3.0: 2024-12-25
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary