7OUF | pdb_00007ouf

Structure of the STLV intasome:B56 complex bound to the strand-transfer inhibitor XZ450


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7OUF

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 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.

Macromolecule Content 

  • Total Structure Weight: 333.44 kDa 
  • Atom Count: 15,094 
  • Modeled Residue Count: 1,744 
  • Deposited Residue Count: 2,714 
  • Unique protein chains: 2
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  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:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoform 3 of PC4 and SFRS1-interacting protein,Isoform Gamma-1 of Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoformC [auth F],
H [auth C]
697Homo sapiensMutation(s): 0 
Gene Names: PSIP1DFS70LEDGFPSIP2PPP2R5CKIAA0044
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) 
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) 
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 H]
28Simian T-lymphotropic virus 1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1L0
(Subject of Investigation/LOI)

Query on 1L0



Download:Ideal Coordinates CCD File
O [auth E],
T [auth B]
4-azanyl-~{N}-[[2,4-bis(fluoranyl)phenyl]methyl]-6-[3-(dimethylamino)-3-oxidanylidene-propyl]-1-oxidanyl-2-oxidanylidene-1,8-naphthyridine-3-carboxamide
C21 H21 F2 N5 O4
BZKKUHPYPOFQBB-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: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTCoot
MODEL REFINEMENTPHENIXdev-4142

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