7UE1 | pdb_00007ue1

HIV-1 Integrase Catalytic Core Domain Mutant (KGD) in Complex with Inhibitor GRL-142

• PDB DOI: https://doi.org/10.2210/pdb7UE1/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-03-21 Released: 2023-03-22 
• Deposition Author(s): Aoki, M., Aoki-Ogata, H., Bulut, H., Hayashi, H., Davis, D., Hasegawa, K., Yarchoan, R., Ghosh, A.K., Pau, A.K., Mitsuya, H.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.317 (Depositor), 0.321 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: experimental

Literature

GRL-142 binds to and impairs HIV-1 integrase nuclear localization signal and potently suppresses highly INSTI-resistant HIV-1 variants.

Aoki, M., Aoki-Ogata, H., Bulut, H., Hayashi, H., Takamune, N., Kishimoto, N., Tanaka, H., Higashi-Kuwata, N., Hattori, S.I., Das, D., Venkateswara Rao, K., Iwama, K., Davis, D.A., Hasegawa, K., Murayama, K., Yarchoan, R., Ghosh, A.K., Pau, A.K., Machida, S., Misumi, S., Mitsuya, H.

(2023) Sci Adv 9: eadg2955-eadg2955

• PubMed: 37436982 
• DOI: https://doi.org/10.1126/sciadv.adg2955
• Primary Citation Related Structures: 
  7UE1


• PubMed Abstract: 
  

  Nuclear localization signal (NLS) of HIV-1 integrase (IN) is implicated in nuclear import of HIV-1 preintegration complex (PIC). Here, we established a multiclass drug-resistant HIV-1 variant (HIV _KGD ) by consecutively exposing an HIV-1 variant to various antiretroviral agents including IN strand transfer inhibitors (INSTIs). HIV _KGD was extremely susceptible to a previously reported HIV-1 protease inhibitor, GRL-142, with IC ₅₀ of 130 femtomolar. When cells were exposed to HIV _KGD IN-containing recombinant HIV in the presence of GRL-142, significant decrease of unintegrated 2-LTR circular cDNA was observed, suggesting that nuclear import of PIC was severely compromised by GRL-142. X-ray crystallographic analyses revealed that GRL-142 interacts with NLS's putative sequence (DQAEHLK) and sterically blocks the nuclear transport of GRL-142-bound HIV _KGD 's PIC. Highly INSTI-resistant HIV-1 variants isolated from heavily INSTI-experienced patients proved to be susceptible to GRL-142, suggesting that NLS-targeting agents would serve as salvage therapy agents for highly INSTI-resistant variant-harboring individuals. The data should offer a new modality to block HIV-1 infectivity and replication and shed light on developing NLS inhibitors for AIDS therapy.

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Organizational Affiliation: 
• Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Department of Medical Technology, Kumamoto Health Science University, Kumamoto, Japan.
Department of Refractory Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan.
Department of Intelligent Network for Infection Control, Tohoku University Graduate School of Medicine, Miyagi, Japan.
Department of infectious Diseases, International Research Institute of Disaster Science, Tohoku University, Miyagi, Japan.
Department of Environmental and Molecular Health Sciences, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan.
Department of Structural Virology, National Center for Global Health and Medicine Research Institute, Tokyo, Japan.
Departments of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, IN, USA.
Viral Oncology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Structural Biology Division, Japan Synchrotron Radiation Research Institute, Hyogo, Japan.
Division of Biomedical Measurements and Diagnostics, Graduate School of Biomedical Engineering, Tohoku University, Miyagi, Japan.
National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
Division of Clinical Sciences, Kumamoto University Hospital, Kumamoto, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 37.14 kDa 
• Atom Count: 2,277 
• Modeled Residue Count: 288 
• Deposited Residue Count: 332 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrase	A, B	166	Human immunodeficiency virus 1	Mutation(s): 0  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7OA (Subject of Investigation/LOI)	C [auth B]	(3S,3aR,5R,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl [(2S,3R)-4-[{[2-(cyclopropylamino)-1,3-benzothiazol-6-yl]sulfonyl}(2-methylpropyl)amino]-1-(3,5-difluorophenyl)-3-hydroxybutan-2-yl]carbamate C33 H40 F2 N4 O7 S2 ARWGTMGGJGADTI-VFGYXJDYSA-N
SO4	D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.317 (Depositor), 0.321 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.368	α = 90
b = 111.368	β = 90
c = 137.288	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-03-22 
Deposition Author(s): Aoki, M., Aoki-Ogata, H., Bulut, H., Hayashi, H., Davis, D., Hasegawa, K., Yarchoan, R., Ghosh, A.K., Pau, A.K., Mitsuya, H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History  

• Version 1.0: 2023-03-22
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.2: 2024-04-24
  Changes: Database references