4B3O | pdb_00004b3o

Structures of HIV-1 RT and RNA-DNA Complex Reveal a Unique RT Conformation and Substrate Interface

• PDB DOI: https://doi.org/10.2210/pdb4B3O/pdb
• NAKB: 4B3O

• Classification: HYDROLASE/DNA/RNA
• Organism(s): Human immunodeficiency virus 1, synthetic construct
• Expression System: Escherichia coli M15
• Mutation(s): Yes 


• Deposited: 2012-07-25 Released: 2013-01-16 
• Deposition Author(s): Lapkouski, M., Tian, L., Miller, J.T., Le Grice, S.F.J., Yang, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.295 (Depositor), 0.298 (DCC) 
• R-Value Work: 
  0.275 (Depositor), 0.277 (DCC) 
• R-Value Observed: 
  0.276 (Depositor) 

Starting Model: experimental

Literature

Complexes of HIV-1 RT, Nnrti and RNA/DNA Hybrid Reveal a Structure Compatible with RNA Degradation

Lapkouski, M., Tian, L., Miller, J.T., Le Grice, S.F.J., Yang, W.

(2013) Nat Struct Mol Biol 20: 230

• PubMed: 23314251 
• DOI: https://doi.org/10.1038/nsmb.2485
• Primary Citation Related Structures: 
  4B3O, 4B3P, 4B3Q


• PubMed Abstract: 
  

  Hundreds of structures of type 1 human immunodeficiency virus (HIV-1) reverse transcriptase (RT) have been determined, but only one contains an RNA/DNA hybrid. Here we report three structures of HIV-1 RT complexed with a non-nucleotide RT inhibitor (NNRTI) and an RNA/DNA hybrid. In the presence of an NNRTI, the RNA/DNA structure differs from all prior nucleic acid-RT structures including the RNA/DNA hybrid. The enzyme structure also differs from all previous RT-DNA complexes. Thus, the hybrid has ready access to the RNase-H active site. These observations indicate that an RT-nucleic acid complex may adopt two structural states, one competent for DNA polymerization and the other for RNA degradation. RT mutations that confer drug resistance but are distant from the inhibitor-binding sites often map to the unique RT-hybrid interface that undergoes conformational changes between two catalytic states.

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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, USA.
HIV Drug Resistance Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 132.11 kDa 
• Atom Count: 8,513 
• Modeled Residue Count: 996 
• Deposited Residue Count: 1,052 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
REVERSE TRANSCRIPTASE/RIBONUCLEASE H	A	560	Human immunodeficiency virus 1	Mutation(s): 7  EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.13 (PDB Primary Data), 3.4.23.16 (PDB Primary Data), 3.1.13.2 (PDB Primary Data)
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
P51 RT	B	441	Human immunodeficiency virus 1	Mutation(s): 3  EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.13 (PDB Primary Data), 3.4.23.16 (PDB Primary Data)
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
5'-D(*CP*GP*TP*AP*TP*GP*CP*CP*TP*AP*TP*AP*GP*TP *TP*AP*TP*TP*GP*TP*GP*GP*CP*C)-3'	C [auth D]	24	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
5'-R(*AP*UP*GP*AP*3DRP*GP*GP*CP*CP*AP*CP*AP*AP*UP*AP *AP*CP*UP*AP*UP*AP*GP*GP*CP*AP*UP*A)-3'	D [auth R]	27	synthetic construct

Small Molecules

Ligands 2 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
CA	F [auth D], G [auth R]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
EFZ	BindingDB:  4B3O	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: 3.30 Å
• R-Value Free:  0.295 (Depositor), 0.298 (DCC) 
• R-Value Work:  0.275 (Depositor), 0.277 (DCC) 
• R-Value Observed: 0.276 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 164.598	α = 90
b = 164.598	β = 90
c = 129.03	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-16 
Deposition Author(s): Lapkouski, M., Tian, L., Miller, J.T., Le Grice, S.F.J., Yang, W.

Revision History  

• Version 1.0: 2013-01-16
  Type: Initial release
  
• Version 1.1: 2013-01-23
  Changes: Database references
• Version 1.2: 2013-02-20
  Changes: Database references
• Version 1.3: 2019-03-06
  Changes: Data collection, Derived calculations, Experimental preparation, Other
• Version 1.4: 2019-05-15
  Changes: Data collection, Experimental preparation
• Version 1.5: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description