6N3J

MicroED Structure of the CTD-SP1 fragment of HIV-1 Gag


Experimental Data Snapshot

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 3 Å
  • Aggregation State: 3D ARRAY 
  • Reconstruction Method: CRYSTALLOGRAPHY 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

MicroED structures of HIV-1 Gag CTD-SP1 reveal binding interactions with the maturation inhibitor bevirimat.

Purdy, M.D.Shi, D.Chrustowicz, J.Hattne, J.Gonen, T.Yeager, M.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: 13258-13263

  • DOI: 10.1073/pnas.1806806115
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • HIV-1 protease (PR) cleavage of the Gag polyprotein triggers the assembly of mature, infectious particles. Final cleavage of Gag occurs at the junction helix between the capsid protein CA and the SP1 spacer peptide. Here we used MicroED to delineate ...

    HIV-1 protease (PR) cleavage of the Gag polyprotein triggers the assembly of mature, infectious particles. Final cleavage of Gag occurs at the junction helix between the capsid protein CA and the SP1 spacer peptide. Here we used MicroED to delineate the binding interactions of the maturation inhibitor bevirimat (BVM) using very thin frozen-hydrated, 3D microcrystals of a CTD-SP1 Gag construct with and without bound BVM. The 2.9-Å MicroED structure revealed that a single BVM molecule stabilizes the six-helix bundle via both electrostatic interactions with the dimethylsuccinyl moiety and hydrophobic interactions with the pentacyclic triterpenoid ring. These results provide insight into the mechanism of action of BVM and related maturation inhibitors that will inform further drug discovery efforts. This study also demonstrates the capabilities of MicroED for structure-based drug design.


    Organizational Affiliation

    Department of Biological Chemistry, University of California, Los Angeles, Los Angeles CA 90095.,Howard Hughes Medical Institute, Los Angeles, CA 90095.,Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, VA 22908.,Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908.,Department of Physiology, University of California, Los Angeles, Los Angeles CA 90095.,Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA 22908.,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147.,Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908; tgonen@ucla.edu yeager@virginia.edu.,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147; tgonen@ucla.edu yeager@virginia.edu.,Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA 22908.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CTD-SP1 fragment of HIV-1 Gag
A, B, C, D, E, F
110Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)Mutation(s): 1 
Gene Names: gag
Find proteins for P04591 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Go to UniProtKB:  P04591
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 3 Å
  • Aggregation State: 3D ARRAY 
  • Reconstruction Method: CRYSTALLOGRAPHY 
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
MOSFLMdata reduction
PDB_EXTRACTdata extraction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United States5 P50 GM082545-10
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM066087
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP50 GM082545
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM12850

Revision History 

  • Version 1.0: 2018-12-12
    Type: Initial release
  • Version 1.1: 2018-12-19
    Type: Data collection, Database references
  • Version 1.2: 2018-12-26
    Type: Data collection, Database references
  • Version 1.3: 2019-01-09
    Type: Data collection, Database references
  • Version 1.4: 2019-12-18
    Type: Author supporting evidence