6BSI | pdb_00006bsi

Structure of HIV-1 RT complexed with an RNA/DNA hybrid containing the polypurine-tract sequence

• PDB DOI: https://doi.org/10.2210/pdb6BSI/pdb
• NAKB: 6BSI

• Classification: viral protein/dna/rna/inhibitor
• Organism(s): Human immunodeficiency virus 1, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-12-03 Released: 2018-01-03 
• Deposition Author(s): Tian, L., Kim, M., Yang, W.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free: 
  0.241 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Literature

Structure of HIV-1 reverse transcriptase cleaving RNA in an RNA/DNA hybrid.

Tian, L., Kim, M.S., Li, H., Wang, J., Yang, W.

(2018) Proc Natl Acad Sci U S A 115: 507-512

• PubMed: 29295939 
• DOI: https://doi.org/10.1073/pnas.1719746115
• Primary Citation Related Structures: 
  6BSG, 6BSH, 6BSI, 6BSJ


• PubMed Abstract: 
  

  HIV-1 reverse transcriptase (RT) contains both DNA polymerase and RNase H activities to convert the viral genomic RNA to dsDNA in infected host cells. Here we report the 2.65-Å resolution structure of HIV-1 RT engaging in cleaving RNA in an RNA/DNA hybrid. A preferred substrate sequence is absolutely required to enable the RNA/DNA hybrid to adopt the distorted conformation needed to interact properly with the RNase H active site in RT. Substituting two nucleotides 4 bp upstream from the cleavage site results in scissile-phosphate displacement by 4 Å. We also have determined the structure of HIV-1 RT complexed with an RNase H-resistant polypurine tract sequence, which adopts a rigid structure and is accommodated outside of the nuclease active site. Based on this newly gained structural information and a virtual drug screen, we have identified an inhibitor specific for the viral RNase H but not for its cellular homologs.

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Organizational Affiliation: 
• Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892.
Integrative Bioscience and Biotechnology, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea.
City of Hope, Duarte, CA 91010.
Richards Center for Structural Biology, Yale University, New Haven, CT 06520.
Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892; [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

Macromolecule Content 

• Total Structure Weight: 131.11 kDa 
• Atom Count: 8,566 
• Modeled Residue Count: 997 
• Deposited Residue Count: 1,047 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
REVERSE TRANSCRIPTASE P66 SUBUNIT	A	558	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: pol
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04585  Go to UniProtKB:  P04585

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
REVERSE TRANSCRIPTASE P51 SUBUNIT	B	441	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: pol
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04585  Go to UniProtKB:  P04585

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*TP*TP*TP*TP*TP*CP*TP*TP*TP*TP*GP*TP*TP*AP*TP*TP*GP*TP*GP*GP*CP*C)-3')	C [auth D]	23	Homo sapiens

Entity ID: 4
Molecule	Chains	Length	Organism	Image
RNA (25-MER)	D [auth R]	25	Homo sapiens

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EFZ	E [auth A]	(-)-6-CHLORO-4-CYCLOPROPYLETHYNYL-4-TRIFLUOROMETHYL-1,4-DIHYDRO-2H-3,1-BENZOXAZIN-2-ONE C14 H9 Cl F3 N O2 XPOQHMRABVBWPR-ZDUSSCGKSA-N
GOL	H [auth D], I [auth R]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	F [auth A], G [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
EFZ	BindingDB:  6BSI	Ki: min: 3, max: 3000 (nM) from 20 assay(s)
		IC50: min: 0.09, max: 910 (nM) from 52 assay(s)
		EC50: min: 1, max: 300 (nM) from 8 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free:  0.241 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 163.85	α = 90
b = 163.85	β = 90
c = 129.57	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-01-03 
Deposition Author(s): Tian, L., Kim, M., Yang, W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	--

Revision History  

• Version 1.0: 2018-01-03
  Type: Initial release
  
• Version 1.1: 2018-01-17
  Changes: Author supporting evidence
• Version 1.2: 2018-04-25
  Changes: Data collection, Database references
• Version 1.3: 2022-03-23
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.4: 2024-05-22
  Changes: Data collection