4ZMJ

Crystal Structure of Ligand-Free BG505 SOSIP.664 HIV-1 Env Trimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.268 

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This is version 2.1 of the entry. See complete history


Literature

Crystal structure, conformational fixation and entry-related interactions of mature ligand-free HIV-1 Env.

Do Kwon, Y.Pancera, M.Acharya, P.Georgiev, I.S.Crooks, E.T.Gorman, J.Joyce, M.G.Guttman, M.Ma, X.Narpala, S.Soto, C.Terry, D.S.Yang, Y.Zhou, T.Ahlsen, G.Bailer, R.T.Chambers, M.Chuang, G.Y.Doria-Rose, N.A.Druz, A.Hallen, M.A.Harned, A.Kirys, T.Louder, M.K.O'Dell, S.Ofek, G.Osawa, K.Prabhakaran, M.Sastry, M.Stewart-Jones, G.B.Stuckey, J.Thomas, P.V.Tittley, T.Williams, C.Zhang, B.Zhao, H.Zhou, Z.Donald, B.R.Lee, L.K.Zolla-Pazner, S.Baxa, U.Schon, A.Freire, E.Shapiro, L.Lee, K.K.Arthos, J.Munro, J.B.Blanchard, S.C.Mothes, W.Binley, J.M.McDermott, A.B.Mascola, J.R.Kwong, P.D.

(2015) Nat Struct Mol Biol 22: 522-531

  • DOI: https://doi.org/10.1038/nsmb.3051
  • Primary Citation of Related Structures:  
    4ZMJ

  • PubMed Abstract: 

    As the sole viral antigen on the HIV-1-virion surface, trimeric Env is a focus of vaccine efforts. Here we present the structure of the ligand-free HIV-1-Env trimer, fix its conformation and determine its receptor interactions. Epitope analyses revealed trimeric ligand-free Env to be structurally compatible with broadly neutralizing antibodies but not poorly neutralizing ones. We coupled these compatibility considerations with binding antigenicity to engineer conformationally fixed Envs, including a 201C 433C (DS) variant specifically recognized by broadly neutralizing antibodies. DS-Env retained nanomolar affinity for the CD4 receptor, with which it formed an asymmetric intermediate: a closed trimer bound by a single CD4 without the typical antigenic hallmarks of CD4 induction. Antigenicity-guided structural design can thus be used both to delineate mechanism and to fix conformation, with DS-Env trimers in virus-like-particle and soluble formats providing a new generation of vaccine antigens.


  • Organizational Affiliation

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp160A [auth G]481Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Explore Q2N0S6 
Go to UniProtKB:  Q2N0S6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp160153Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Explore Q2N0S6 
Go to UniProtKB:  Q2N0S6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S6
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-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-glucopyranoseC [auth A]6N-Glycosylation
Glycosylation Resources
GlyTouCan:  G56014GC
GlyCosmos:  G56014GC
GlyGen:  G56014GC
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth C],
E [auth D]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth G]
G
H [auth G]
I [auth G]
J [auth G]
F [auth G],
G,
H [auth G],
I [auth G],
J [auth G],
K [auth G],
L [auth G],
M [auth G],
N [auth G],
O [auth G],
P [auth G],
Q [auth G],
R [auth B],
S [auth B],
T [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.268 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.18α = 90
b = 107.18β = 90
c = 103.06γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-24
    Type: Initial release
  • Version 1.1: 2015-07-08
    Changes: Database references
  • Version 1.2: 2015-07-29
    Changes: Database references
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence, Derived calculations, Source and taxonomy
  • Version 1.4: 2019-12-11
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary