8FNH | pdb_00008fnh

Structure of Q148K HIV-1 intasome with Dolutegravir bound

• PDB DOI: https://doi.org/10.2210/pdb8FNH/pdb
• EM Map EMD-29313: EMDB EMDataResource
• NAKB: 8FNH

• Classification: VIRAL PROTEIN/DNA/INHIBITOR
• Organism(s): Homo sapiens, Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-12-27 Released: 2023-08-09 
• Deposition Author(s): Shan, Z.L., Passos, D.O., Strutzenberg, T.S., Li, M., Lyumkis, D.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants.

Li, M., Oliveira Passos, D., Shan, Z., Smith, S.J., Sun, Q., Biswas, A., Choudhuri, I., Strutzenberg, T.S., Haldane, A., Deng, N., Li, Z., Zhao, X.Z., Briganti, L., Kvaratskhelia, M., Burke Jr., T.R., Levy, R.M., Hughes, S.H., Craigie, R., Lyumkis, D.

(2023) Sci Adv 9: eadg5953-eadg5953

• PubMed: 37478179 
• DOI: https://doi.org/10.1126/sciadv.adg5953
• Primary Citation Related Structures: 
  8FN7, 8FND, 8FNG, 8FNH, 8FNJ, 8FNL, 8FNM, 8FNN, 8FNO, 8FNP, 8FNQ


• PubMed Abstract: 
  

  HIV-1 infection depends on the integration of viral DNA into host chromatin. Integration is mediated by the viral enzyme integrase and is blocked by integrase strand transfer inhibitors (INSTIs), first-line antiretroviral therapeutics widely used in the clinic. Resistance to even the best INSTIs is a problem, and the mechanisms of resistance are poorly understood. Here, we analyze combinations of the mutations E138K, G140A/S, and Q148H/K/R, which confer resistance to INSTIs. The investigational drug 4d more effectively inhibited the mutants compared with the approved drug Dolutegravir (DTG). We present 11 new cryo-EM structures of drug-resistant HIV-1 intasomes bound to DTG or 4d, with better than 3-Å resolution. These structures, complemented with free energy simulations, virology, and enzymology, explain the mechanisms of DTG resistance involving E138K + G140A/S + Q148H/K/R and show why 4d maintains potency better than DTG. These data establish a foundation for further development of INSTIs that potently inhibit resistant forms in integrase.

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Organizational Affiliation: 
• National Institute of Diabetes and Digestive Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA.
Center for Biophysics and Computational Biology, and Department of Chemistry, Temple University, Philadelphia, PA 19122, USA.
Center for Biophysics and Computational Biology and Department of Physics, Temple University, Philadelphia, PA 19122, USA.
Department of Chemistry and Physical Sciences, Pace University, New York, NY, 10038, USA.
Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
Graduate School of Biological Sciences, Section of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A4B2C2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 8-mer - A4B4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 352.18 kDa 
• Atom Count: 11,988 
• Modeled Residue Count: 1,304 
• Deposited Residue Count: 3,016 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lamina-associated polypeptide 2, isoform alpha,Integrase chimera	A, B, C, D, G, H, I, J	364	Homo sapiens, Human immunodeficiency virus 1 This entity is chimeric	Mutation(s): 1  Gene Names: TMPO, LAP2, gag-pol EC: 2.7.7 (PDB Primary Data), 3.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12497  Go to UniProtKB:  P12497
Find proteins for P42166 (Homo sapiens) Explore P42166  Go to UniProtKB:  P42166
PHAROS:  P42166 GTEx:  ENSG00000120802
UniProt Groups	P12497P42166

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (27-MER)	E, K	27	Human immunodeficiency virus 1

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (25-MER)	F, L	25	Human immunodeficiency virus 1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DLU (Subject of Investigation/LOI)	P [auth A], T [auth G]	(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	O [auth A], S [auth G]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	M [auth A], N [auth A], Q [auth G], R [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	3

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-08-09 
Deposition Author(s): Shan, Z.L., Passos, D.O., Strutzenberg, T.S., Li, M., Lyumkis, D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U01 AI136680
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI146017
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U54 AI170855
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM132090
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM148049

Revision History  

• Version 1.0: 2023-08-09
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Structure summary