8CT5 | pdb_00008ct5

Catalytic Core Domain of HIV-1 Integrase (F185K)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 
    0.236 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8CT5

This is version 1.3 of the entry. See complete history

Literature

Structure of a HIV-1 IN-Allosteric inhibitor complex at 2.93 angstrom resolution: Routes to inhibitor optimization.

Eilers, G.Gupta, K.Allen, A.Montermoso, S.Murali, H.Sharp, R.Hwang, Y.Bushman, F.D.Van Duyne, G.

(2023) PLoS Pathog 19: e1011097-e1011097

  • DOI: https://doi.org/10.1371/journal.ppat.1011097
  • Primary Citation Related Structures: 
    8CT5, 8CT7, 8CTA

  • PubMed Abstract: 

    HIV integrase (IN) inserts viral DNA into the host genome and is the target of the strand transfer inhibitors (STIs), a class of small molecules currently in clinical use. Another potent class of antivirals is the allosteric inhibitors of integrase, or ALLINIs. ALLINIs promote IN aggregation by stabilizing an interaction between the catalytic core domain (CCD) and carboxy-terminal domain (CTD) that undermines viral particle formation in late replication. Ongoing challenges with inhibitor potency, toxicity, and viral resistance motivate research to understand their mechanism. Here, we report a 2.93 Å X-ray crystal structure of the minimal ternary complex between CCD, CTD, and the ALLINI BI-224436. This structure reveals an asymmetric ternary complex with a prominent network of π-mediated interactions that suggest specific avenues for future ALLINI development and optimization.


  • Organizational Affiliation
    • Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.

Macromolecule Content 

  • Total Structure Weight: 18.28 kDa 
  • Atom Count: 1,165 
  • Modeled Residue Count: 143 
  • Deposited Residue Count: 161 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Integrase161Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: pol
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12497 
Go to UniProtKB:  P12497
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12497
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free:  0.236 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.973α = 90
b = 72.973β = 90
c = 66.097γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 AI 052845

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-15
    Type: Initial release
  • Version 1.1: 2023-03-15
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-30
    Changes: Structure summary