6RWL

SIVrcm intasome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.36 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of second-generation HIV integrase inhibitor action and viral resistance.

Cook, N.J.Li, W.Berta, D.Badaoui, M.Ballandras-Colas, A.Nans, A.Kotecha, A.Rosta, E.Engelman, A.N.Cherepanov, P.

(2020) Science 367: 806-810

  • DOI: 10.1126/science.aay4919
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Although second-generation HIV integrase strand-transfer inhibitors (INSTIs) are prescribed throughout the world, the mechanistic basis for the superiority of these drugs is poorly understood. We used single-particle cryo-electron microscopy to visua ...

    Although second-generation HIV integrase strand-transfer inhibitors (INSTIs) are prescribed throughout the world, the mechanistic basis for the superiority of these drugs is poorly understood. We used single-particle cryo-electron microscopy to visualize the mode of action of the advanced INSTIs dolutegravir and bictegravir at near-atomic resolution. Glutamine-148→histidine (Q148H) and glycine-140→serine (G140S) amino acid substitutions in integrase that result in clinical INSTI failure perturb optimal magnesium ion coordination in the enzyme active site. The expanded chemical scaffolds of second-generation compounds mediate interactions with the protein backbone that are critical for antagonizing viruses containing the Q148H and G140S mutations. Our results reveal that binding to magnesium ions underpins a fundamental weakness of the INSTI pharmacophore that is exploited by the virus to engender resistance and provide a structural framework for the development of this class of anti-HIV/AIDS therapeutics.


    Organizational Affiliation

    Department of Infectious Disease, Imperial College London, St Mary's Campus, London W2 1PG, UK.,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.,Structural Biology Science Technology Platform, Francis Crick Institute, London NW1 1AT, UK.,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA. peter.cherepanov@crick.ac.uk alan_engelman@dfci.harvard.edu.,Chromatin Structure and Mobile DNA Laboratory, Francis Crick Institute, London NW1 1AT, UK.,Materials and Structural Analysis, Thermo Fisher Scientific, Eindhoven, 5651 GG, Netherlands.,Department of Chemistry, King's College London, London SE1 1DB, UK.,Chromatin Structure and Mobile DNA Laboratory, Francis Crick Institute, London NW1 1AT, UK. peter.cherepanov@crick.ac.uk alan_engelman@dfci.harvard.edu.,The Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pol protein
A, B, C, M, I, J, K, E
290Simian immunodeficiency virusMutation(s): 1 
Gene Names: pol
Find proteins for E1ANT8 (Simian immunodeficiency virus)
Go to UniProtKB:  E1ANT8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Pol protein
D, L
289Simian immunodeficiency virusMutation(s): 1 
Gene Names: pol
Find proteins for E1ANT8 (Simian immunodeficiency virus)
Go to UniProtKB:  E1ANT8
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Pol protein
F, N
290Simian immunodeficiency virusMutation(s): 0 
Gene Names: pol
Find proteins for E1ANT8 (Simian immunodeficiency virus)
Go to UniProtKB:  E1ANT8
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*CP*TP*AP*AP*GP*AP*AP*AP*AP*AP*TP*CP*TP*CP*TP*AP*CP*CP*A)-3')T,W30Simian immunodeficiency virus
Entity ID: 5
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*AP*CP*TP*GP*GP*TP*AP*GP*AP*GP*AP*TP*TP*TP*TP*TP*CP*TP*TP*AP*GP*C)-3')S,Q33Simian immunodeficiency virus
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, E, I, J, K, M
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.36 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 General Medical SciencesUnited StatesGM082251
The Francis Crick InstituteUnited KingdomFC001061

Revision History 

  • Version 1.0: 2020-02-05
    Type: Initial release
  • Version 1.1: 2020-02-19
    Type: Database references
  • Version 1.2: 2020-02-26
    Type: Database references, Structure summary