6OPQ

CD4- and 17-bound HIV-1 Env B41 SOSIP frozen with LMNG


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A Strain-Specific Inhibitor of Receptor-Bound HIV-1 Targets a Pocket near the Fusion Peptide.

Ozorowski, G.Torres, J.L.Santos-Martins, D.Forli, S.Ward, A.B.

(2020) Cell Rep 33: 108428-108428

  • DOI: https://doi.org/10.1016/j.celrep.2020.108428
  • Primary Citation of Related Structures:  
    6OPN, 6OPO, 6OPP, 6OPQ, 6X5B, 6X5C

  • PubMed Abstract: 

    Disruption of viral fusion represents a viable, albeit under-explored, target for HIV therapeutics. Here, while studying the receptor-bound envelope glycoprotein conformation by cryoelectron microscopy (cryo-EM), we identify a pocket near the base of the trimer containing a bound detergent molecule and perform in silico drug screening by using a library of drug-like and commercially available molecules. After down-selection, we solve cryo-EM structures that validate the binding of two small molecule hits in very similar manners to the predicted binding poses, including interactions with aromatic residues within the fusion peptide. One of the molecules demonstrates low micromolar inhibition of the autologous virus by using a very rare phenylalanine in the fusion peptide and stabilizing the surrounding region. This work demonstrates that small molecules can target the fusion process, providing an additional target for anti-HIV therapeutics, and highlights the need to explore how fusion peptide sequence variations affect receptor-mediated conformational states across diverse HIV strains.


  • Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, International AIDS Vaccine Initiative Neutralizing Antibody Center, and Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp160A,
F [auth D],
K [auth E]
524Human immunodeficiency virus 1Mutation(s): 5 
Gene Names: env
UniProt
Find proteins for B3UES2 (Human immunodeficiency virus 1)
Explore B3UES2 
Go to UniProtKB:  B3UES2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3UES2
Glycosylation
Glycosylation Sites: 12
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
17b Fab light chainB [auth L],
G [auth N],
L [auth O]
214Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp41C [auth B],
H [auth F],
M [auth G]
153Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: env
UniProt
Find proteins for B3UEZ6 (Human immunodeficiency virus 1)
Explore B3UEZ6 
Go to UniProtKB:  B3UEZ6
Entity Groups  
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UniProt GroupB3UEZ6
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD4D [auth C],
I,
N [auth J]
208Homo sapiensMutation(s): 0 
Gene Names: CD4
UniProt & NIH Common Fund Data Resources
Find proteins for P01730 (Homo sapiens)
Explore P01730 
Go to UniProtKB:  P01730
PHAROS:  P01730
GTEx:  ENSG00000010610 
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UniProt GroupP01730
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
17b Fab heavy chainE [auth H],
J [auth K],
O [auth M]
229Homo sapiensMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-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-glucopyranoseIA [auth i],
Q,
Z
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42227JK
GlyCosmos:  G42227JK
GlyGen:  G42227JK
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
QA [auth A]
RA [auth A]
SA [auth A]
TA [auth D]
UA [auth D]
QA [auth A],
RA [auth A],
SA [auth A],
TA [auth D],
UA [auth D],
VA [auth D],
WA [auth E],
XA [auth E],
YA [auth E]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTRosetta3.10
MODEL REFINEMENTCoot0.9-pre
RECONSTRUCTIONcryoSPARC2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States109718-63-RKNT
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM069832
Bill & Melinda Gates FoundationUnited StatesOPP1115782

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-21
    Type: Initial release
  • Version 1.1: 2020-12-09
    Changes: Database references