8X22 | pdb_00008x22

HIV-1 reverse transcriptase mutant Q151M/Y115F/F116Y/L74V:DNA:dGTP ternary complex

• PDB DOI: https://doi.org/10.2210/pdb8X22/pdb
• NAKB: 8X22

• Classification: TRANSFERASE
• Organism(s): Human immunodeficiency virus 1, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-11-09 Released: 2024-07-17 
• Deposition Author(s): Yasutake, Y., Hattori, S.I., Mitsuya, H.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free: 
  0.219 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Deviated binding of anti-HBV nucleoside analog E-CFCP-TP to the reverse transcriptase active site attenuates the effect of drug-resistant mutations.

Yasutake, Y., Hattori, S.I., Kumamoto, H., Tamura, N., Maeda, K., Mitsuya, H.

(2024) Sci Rep 14: 15742-15742

• PubMed: 38977798 
• DOI: https://doi.org/10.1038/s41598-024-66505-z
• Primary Citation Related Structures: 
  8X1Z, 8X20, 8X21, 8X22


• PubMed Abstract: 
  

  While certain human hepatitis B virus-targeting nucleoside analogs (NAs) serve as crucial anti-HBV drugs, HBV yet remains to be a major global health threat. E-CFCP is a 4'-modified and fluoromethylenated NA that exhibits potent antiviral activity against both wild-type and drug-resistant HBVs but less potent against human immunodeficiency virus type-1 (HIV-1). Here, we show that HIV-1 with HBV-associated amino acid substitutions introduced into the RT's dNTP-binding site (N-site) is highly susceptible to E-CFCP. We determined the X-ray structures of HBV-associated HIV-1 RT mutants complexed with DNA:E-CFCP-triphosphate (E-CFCP-TP). The structures revealed that exocyclic fluoromethylene pushes the Met184 sidechain backward, and the resultant enlarged hydrophobic pocket accommodates both the fluoromethylene and 4'-cyano moiety of E-CFCP. Structural comparison with the DNA:dGTP/entecavir-triphosphate complex also indicated that the cyclopentene moiety of the bound E-CFCP-TP is slightly skewed and deviated. This positioning partly corresponds to that of the bound dNTP observed in the HIV-1 RT mutant with drug-resistant mutations F160M/M184V, resulting in the attenuation of the structural effects of F160M/M184V substitutions. These results expand our knowledge of the interactions between NAs and the RT N-site and should help further design antiviral NAs against both HIV-1 and HBV.

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Organizational Affiliation: 
• Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, 062-8517, Japan. [e-mail].
Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), AIST, Tokyo, 169-8555, Japan. [e-mail].
National Center for Global Health and Medicine (NCGM) Research Institute, Tokyo, 162-8655, Japan.
Department of Pharmaceutical Sciences, Nihon Pharmaceutical University, Saitama, 362-0806, Japan.
Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, 062-8517, Japan.
Division of Antiviral Therapy, Joint Research Center for Human Retrovirus Infection, Kagoshima University, Kagoshima, 890-8544, Japan.
National Center for Global Health and Medicine (NCGM) Research Institute, Tokyo, 162-8655, Japan. [e-mail].
Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA. [e-mail].
Department of Clinical Sciences, Kumamoto University Hospital, Kumamoto, 860-8556, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 256.83 kDa 
• Atom Count: 17,744 
• Modeled Residue Count: 1,991 
• Deposited Residue Count: 2,078 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pol protein (Fragment)	A, D [auth C]	557	Human immunodeficiency virus 1	Mutation(s): 6  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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 RT p51 subunit	B, E [auth D]	444	Human immunodeficiency virus 1	Mutation(s): 2
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12497  Go to UniProtKB:  P12497

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA/RNA (38-MER)	C [auth E], F	38	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGT (Subject of Investigation/LOI)	G [auth A], L [auth C]	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 HAAZLUGHYHWQIW-KVQBGUIXSA-N
GOL	I [auth A], J [auth A], K [auth B], N [auth C], O [auth D], P [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	H [auth A], M [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free:  0.219 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 285.227	α = 90
b = 285.227	β = 90
c = 96.075	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-07-17 
Deposition Author(s): Yasutake, Y., Hattori, S.I., Mitsuya, H.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP21fk0310113

Revision History  

• Version 1.0: 2024-07-17
  Type: Initial release