3V4I | pdb_00003v4i

Crystal structure of HIV-1 reverse transcriptase (RT) with DNA and AZTTP

• PDB DOI: https://doi.org/10.2210/pdb3V4I/pdb
• NAKB: 3V4I

• Classification: TRANSFERASE/DNA
• Organism(s): Human immunodeficiency virus type 1 BH10
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-12-15 Released: 2012-01-18 
• Deposition Author(s): Das, K., Martinez, S.E., Arnold, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.262 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

HIV-1 reverse transcriptase complex with DNA and nevirapine reveals non-nucleoside inhibition mechanism.

Das, K., Martinez, S.E., Bauman, J.D., Arnold, E.

(2012) Nat Struct Mol Biol 19: 253-259

• PubMed: 22266819 
• DOI: https://doi.org/10.1038/nsmb.2223
• Primary Citation Related Structures: 
  3V4I, 3V6D, 3V81


• PubMed Abstract: 
  

  Combinations of nucleoside and non-nucleoside inhibitors (NNRTIs) of HIV-1 reverse transcriptase (RT) are widely used in anti-AIDS therapies. Five NNRTIs, including nevirapine, are clinical drugs; however, the molecular mechanism of inhibition by NNRTIs is not clear. We determined the crystal structures of RT-DNA-nevirapine, RT-DNA, and RT-DNA-AZT-triphosphate complexes at 2.85-, 2.70- and 2.80-Å resolution, respectively. The RT-DNA complex in the crystal could bind nevirapine or AZT-triphosphate but not both. Binding of nevirapine led to opening of the NNRTI-binding pocket. The pocket formation caused shifting of the 3' end of the DNA primer by ~5.5 Å away from its polymerase active site position. Nucleic acid interactions with fingers and palm subdomains were reduced, the dNTP-binding pocket was distorted and the thumb opened up. The structures elucidate complementary roles of nucleoside and non-nucleoside inhibitors in inhibiting RT.

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Organizational Affiliation: 
• Center for Advanced Biotechnology and Medicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 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)

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: 259 kDa 
• Atom Count: 17,696 
• Modeled Residue Count: 2,022 
• Deposited Residue Count: 2,064 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 Reverse Transcriptase P66 subunit	A, C	556	Human immunodeficiency virus type 1 BH10	Mutation(s): 3  Gene Names: gag-pol EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data)
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366  Go to UniProtKB:  P03366

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 Reverse Transcriptase P51 subunit	B, D	428	Human immunodeficiency virus type 1 BH10	Mutation(s): 1  Gene Names: gag-pol EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data)
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366  Go to UniProtKB:  P03366

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*TP*GP*GP*AP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3')	E [auth T], F [auth E]	27	N/A

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(ATM))-3')	G [auth P], H [auth F]	21	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AZT	J [auth A], L [auth C]	3'-AZIDO-3'-DEOXYTHYMIDINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 GLWHPRRGGYLLRV-XLPZGREQSA-N
MG	I [auth A], K [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.262 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.053	α = 90
b = 132.647	β = 98.12
c = 138.014	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-18 
Deposition Author(s): Das, K., Martinez, S.E., Arnold, E.

Revision History  

• Version 1.0: 2012-01-18
  Type: Initial release
  
• Version 1.1: 2012-01-25
  Changes: Derived calculations
• Version 1.2: 2012-02-15
  Changes: Database references
• Version 1.3: 2017-11-08
  Changes: Refinement description
• Version 1.4: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-10-30
  Changes: Structure summary