7OUG

STLV-1 intasome:B56 in complex with the strand-transfer inhibitor raltegravir


Experimental Data Snapshot

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

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for the inhibition of HTLV-1 integration inferred from cryo-EM deltaretroviral intasome structures.

Barski, M.S.Vanzo, T.Zhao, X.Z.Smith, S.J.Ballandras-Colas, A.Cronin, N.B.Pye, V.E.Hughes, S.H.Burke Jr., T.R.Cherepanov, P.Maertens, G.N.

(2021) Nat Commun 12: 4996-4996

  • DOI: https://doi.org/10.1038/s41467-021-25284-1
  • Primary Citation of Related Structures:  
    7OUF, 7OUG, 7OUH

  • PubMed Abstract: 

    Between 10 and 20 million people worldwide are infected with the human T-cell lymphotropic virus type 1 (HTLV-1). Despite causing life-threatening pathologies there is no therapeutic regimen for this deltaretrovirus. Here, we screened a library of integrase strand transfer inhibitor (INSTI) candidates built around several chemical scaffolds to determine their effectiveness in limiting HTLV-1 infection. Naphthyridines with substituents in position 6 emerged as the most potent compounds against HTLV-1, with XZ450 having highest efficacy in vitro. Using single-particle cryo-electron microscopy we visualised XZ450 as well as the clinical HIV-1 INSTIs raltegravir and bictegravir bound to the active site of the deltaretroviral intasome. The structures reveal subtle differences in the coordination environment of the Mg 2+ ion pair involved in the interaction with the INSTIs. Our results elucidate the binding of INSTIs to the HTLV-1 intasome and support their use for pre-exposure prophylaxis and possibly future treatment of HTLV-1 infection.


  • Organizational Affiliation

    Imperial College London, St. Mary's Hospital, Department of Infectious Disease, Section of Virology, Norfolk Place, London, UK.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IntegraseA [auth D],
B [auth E],
F [auth A],
G [auth B]
301Simian T-lymphotropic virus 1Mutation(s): 1 
Gene Names: pol
UniProt
Find proteins for Q4QY51 (Simian T-lymphotropic virus 1)
Explore Q4QY51 
Go to UniProtKB:  Q4QY51
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4QY51
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 3 of PC4 and SFRS1-interacting protein,Isoform Gamma-2 of Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoformC [auth F],
H [auth C]
697Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O75475 (Homo sapiens)
Explore O75475 
Go to UniProtKB:  O75475
PHAROS:  O75475
GTEx:  ENSG00000164985 
Find proteins for Q13362 (Homo sapiens)
Explore Q13362 
Go to UniProtKB:  Q13362
PHAROS:  Q13362
GTEx:  ENSG00000078304 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ13362O75475
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*CP*TP*GP*TP*GP*TP*TP*TP*GP*GP*CP*GP*CP*TP*TP*CP*TP*CP*TP*C)-3')D [auth I],
I [auth K]
30Simian T-lymphotropic virus 1
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*AP*GP*AP*GP*AP*AP*GP*CP*GP*CP*CP*AP*AP*AP*CP*AP*CP*A)-3')E [auth J],
J [auth L]
28Simian T-lymphotropic virus 1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RLT (Subject of Investigation/LOI)
Query on RLT

Download Ideal Coordinates CCD File 
O [auth E],
T [auth B]
N-(4-fluorobenzyl)-5-hydroxy-1-methyl-2-(1-methyl-1-{[(5-methyl-1,3,4-oxadiazol-2-yl)carbonyl]amino}ethyl)-6-oxo-1,6-di hydropyrimidine-4-carboxamide
C20 H21 F N6 O5
CZFFBEXEKNGXKS-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
K [auth D],
L [auth E],
P [auth A],
Q [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
M [auth E],
N [auth E],
R [auth B],
S [auth B]
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 REFINEMENTCoot0.8.9.2
MODEL REFINEMENTPHENIXdev-4142
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom107005/Z/15Z
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesGM082251
The Francis Crick InstituteUnited KingdomFC001061
Wellcome TrustUnited Kingdom206175/Z/17/Z

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-18
    Type: Initial release
  • Version 1.1: 2021-10-06
    Changes: Data collection, Database references
  • Version 1.2: 2024-07-17
    Changes: Data collection, Refinement description