8TGO | pdb_00008tgo

Crystal structure of the BG505 triple tandem trimer gp140 HIV-1 Env in complex with PGT124 and 35O22


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.75 Å
  • R-Value Free: 
    0.292 (Depositor), 0.286 (DCC) 
  • R-Value Work: 
    0.242 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 
    0.244 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Triple tandem trimer immunogens for HIV-1 and influenza nucleic acid-based vaccines.

Del Moral-Sanchez, I.Wee, E.G.Xian, Y.Lee, W.H.Allen, J.D.Torrents de la Pena, A.Froes Rocha, R.Ferguson, J.Leon, A.N.Koekkoek, S.Schermer, E.E.Burger, J.A.Kumar, S.Zwolsman, R.Brinkkemper, M.Aartse, A.Eggink, D.Han, J.Yuan, M.Crispin, M.Ozorowski, G.Ward, A.B.Wilson, I.A.Hanke, T.Sliepen, K.Sanders, R.W.

(2024) NPJ Vaccines 9: 74-74

  • DOI: https://doi.org/10.1038/s41541-024-00862-8
  • Primary Citation Related Structures: 
    8TGO

  • PubMed Abstract: 

    Recombinant native-like HIV-1 envelope glycoprotein (Env) trimers are used in candidate vaccines aimed at inducing broadly neutralizing antibodies. While state-of-the-art SOSIP or single-chain Env designs can be expressed as native-like trimers, undesired monomers, dimers and malformed trimers that elicit non-neutralizing antibodies are also formed, implying that these designs could benefit from further modifications for gene-based vaccination approaches. Here, we describe the triple tandem trimer (TTT) design, in which three Env protomers are genetically linked in a single open reading frame and express as native-like trimers. Viral vectored Env TTT induced similar neutralization titers but with a higher proportion of trimer-specific responses. The TTT design was also applied to generate influenza hemagglutinin (HA) trimers without the need for trimerization domains. Additionally, we used TTT to generate well-folded chimeric Env and HA trimers that harbor protomers from three different strains. In summary, the TTT design is a useful platform for the design of HIV-1 Env and influenza HA immunogens for a multitude of vaccination strategies.


  • Organizational Affiliation
    • Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.

Macromolecule Content 

  • Total Structure Weight: 476.18 kDa 
  • Atom Count: 29,645 
  • Modeled Residue Count: 3,611 
  • Deposited Residue Count: 4,167 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp41A [auth B],
F [auth H],
K [auth a]
164Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1)
Explore Q2N0S6 
Go to UniProtKB:  Q2N0S6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S6
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
35O22 scFvB [auth D],
G [auth L],
L [auth b]
286Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
PGT124 light chainC,
H [auth P],
M [auth c]
214Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp120D [auth G],
I [auth R],
N [auth e]
490Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1)
Explore Q2N0S6 
Go to UniProtKB:  Q2N0S6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S6
Glycosylation
Glycosylation Sites: 14
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
PGT124 heavy chainE [auth O],
J [auth S],
O [auth f]
235Homo sapiensMutation(s): 0 

Oligosaccharides

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Entity ID: 6
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-glucopyranoseP [auth A]5N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO
GlyCosmos: G22768VO
GlyGen: G22768VO
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-glucopyranose
BA [auth Y],
CA [auth Z],
JA [auth m],
KA [auth n],
R [auth I],
BA [auth Y],
CA [auth Z],
JA [auth m],
KA [auth n],
R [auth I],
S [auth J]
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 9
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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-glucopyranoseFA [auth i],
NA [auth q],
V [auth N]
10N-Glycosylation
Glycosylation Resources
GlyTouCan: G40702WU
GlyCosmos: G40702WU
GlyGen: G40702WU
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-glucopyranoseHA [auth k],
Y [auth V]
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD
GlyCosmos: G81315DD
GlyGen: G81315DD

Small Molecules

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

Query on NAG



Download:Ideal Coordinates CCD File
AB [auth H]
BB [auth H]
CB [auth H]
DB [auth R]
EB [auth R]
AB [auth H],
BB [auth H],
CB [auth H],
DB [auth R],
EB [auth R],
FB [auth R],
GB [auth R],
HB [auth R],
IB [auth R],
JB [auth a],
KB [auth a],
LB [auth a],
MB [auth e],
NB [auth e],
OB [auth e],
PA [auth B],
PB [auth e],
QA [auth B],
QB [auth e],
RA [auth B],
RB [auth e],
SA [auth G],
SB [auth e],
TA [auth G],
TB [auth e],
UA [auth G],
VA [auth G],
WA [auth G],
XA [auth G],
YA [auth G],
ZA [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: 5.75 Å
  • R-Value Free:  0.292 (Depositor), 0.286 (DCC) 
  • R-Value Work:  0.242 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 0.244 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 357.592α = 90
b = 212.044β = 125.07
c = 207.71γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Union (EU)European Union681137
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI110657
International AIDS Vaccine InitiativeUnited States--
Bill & Melinda Gates FoundationUnited StatesOPP1111923
Bill & Melinda Gates FoundationUnited StatesOPP1132237
Bill & Melinda Gates FoundationUnited StatesOPP1115782

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-17
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Structure summary