6RWN

SIVrcm intasome in complex with dolutegravir


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1126/science.aay4919
  • Primary Citation of Related Structures:  
    6RWL, 6RWM, 6RWN, 6RWO

  • 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 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

    Chromatin Structure and Mobile DNA Laboratory, Francis Crick Institute, London NW1 1AT, UK.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pol protein290Simian immunodeficiency virusMutation(s): 1 
Gene Names: pol
UniProt
Find proteins for E1ANT8 (Simian immunodeficiency virus)
Explore E1ANT8 
Go to UniProtKB:  E1ANT8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE1ANT8
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
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')B [auth Q],
J [auth S]
33Simian immunodeficiency virus
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
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')C [auth W],
K [auth T]
30Simian immunodeficiency virus
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DLU (Subject of Investigation/LOI)
Query on DLU

Download Ideal Coordinates CCD File 
AA [auth I],
S [auth A]
(4R,12aS)-N-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6,8-dioxo-3,4,6,8,12,12a-hexahydro-2H-pyrido[1',2':4,5]pyrazino[2,1-b][1,3]oxazine-9-carboxamide
C20 H19 F2 N3 O5
RHWKPHLQXYSBKR-BMIGLBTASA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
DA [auth M]
EA [auth C]
FA [auth B]
Q [auth A]
V [auth E]
DA [auth M],
EA [auth C],
FA [auth B],
Q [auth A],
V [auth E],
W [auth K],
X [auth J],
Y [auth I]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
R [auth A],
Z [auth I]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth I],
CA [auth I],
T [auth A],
U [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTCoot
MODEL REFINEMENTPHENIX1.15.2-3472
RECONSTRUCTIONcryoSPARC2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM082251
The Francis Crick InstituteUnited KingdomFC001061

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-05
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Database references
  • Version 1.2: 2020-02-26
    Changes: Database references, Structure summary
  • Version 1.3: 2022-03-30
    Changes: Author supporting evidence, Database references