6PUZ

Structure of HIV cleaved synaptic complex (CSC) intasome bound with magnesium and INSTI XZ446 (compound 4f)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis for strand transfer inhibitor binding to HIV intasomes.

Passos, D.O.Li, M.Jozwik, I.K.Zhao, X.Z.Santos-Martins, D.Yang, R.Smith, S.J.Jeon, Y.Forli, S.Hughes, S.H.Burke Jr., T.R.Craigie, R.Lyumkis, D.

(2020) Science --: --

  • DOI: 10.1126/science.aay8015
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The HIV intasome is a large nucleoprotein assembly that mediates the integration of a DNA copy of the viral genome into host chromatin. Intasomes are targeted by the latest generation of antiretrovirals, integrase (IN) strand transfer inhibitors (INS ...

    The HIV intasome is a large nucleoprotein assembly that mediates the integration of a DNA copy of the viral genome into host chromatin. Intasomes are targeted by the latest generation of antiretrovirals, integrase (IN) strand transfer inhibitors (INSTIs). Challenges associated with lentiviral intasome biochemistry have hindered high-resolution structural studies of how INSTIs bind to their native drug target. Here, we present high-resolution cryo-electron microscopy (cryo-EM) structures of HIV intasomes bound to the latest generation INSTIs. These structures highlight how small changes in the IN active site can have significant implications for drug binding and design and provide mechanistic insights into why a leading INSTI retains efficacy against a broad spectrum of drug resistant variants. The data have implications for expanding effective treatments available for HIV-infected individuals.


    Organizational Affiliation

    Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.,The Salk Institute for Biological Studies, Laboratory of Genetics, La Jolla, CA 92037, USA. dlyumkis@salk.edu.,National Institutes of Health, National Institute of Diabetes and Digestive Diseases, Bethesda, MD 20892, USA.,The Salk Institute for Biological Studies, Laboratory of Genetics, La Jolla, CA 92037, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chimeric Sso7d and HIV-1 integrase
A, B, C, D
383Human immunodeficiency virus 1Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
This entity is chimeric
Mutation(s): 0 
Gene Names: sso7d (sso7d-1)
Find proteins for Q76353 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q76353
Find proteins for P39476 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Go to UniProtKB:  P39476
Entity ID: 2
MoleculeChainsLengthOrganism
viral DNA non-transferred strandE27Human immunodeficiency virus 1
Entity ID: 3
MoleculeChainsLengthOrganism
viral DNA transferred strandF25Human immunodeficiency virus 1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
XXJ
Query on XXJ

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Download CCD File 
A
4-azanyl-N-[[2,4-bis(fluoranyl)phenyl]methyl]-1-oxidanyl-2-oxidanylidene-6-[2-(phenylsulfonyl)ethyl]-1,8-naphthyridine-3-carboxamide
C24 H20 F2 N4 O5 S
GNATXMRYUGEZME-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI136680
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM069832
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI146017

Revision History 

  • Version 1.0: 2020-02-12
    Type: Initial release