3V81

Crystal structure of HIV-1 reverse transcriptase (RT) with DNA and the nonnucleoside inhibitor nevirapine

DOI: 10.2210/pdb3V81/pdb
NDB: NA1483

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

Deposited: 2011-12-22 Released: 2012-01-18
Deposition Author(s): Das, K., Martinez, S.E., Arnold, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.298
R-Value Work: 0.251
R-Value Observed: 0.252

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: 10.1038/nsmb.2223
Primary Citation of 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.

Related Citations:

Structural basis for the role of the K65R mutation in HIV-1 reverse transcriptase polymerization, excision antagonism, and tenofovir resistance.
Das, K., Bandwar, R.P., White, K.L., Feng, J.Y., Sarafianos, S.G., Tuske, S., Tu, X., Clark, A.D., Boyer, P.L., Hou, X., Gaffney, B.L., Jones, R.A., Miller, M.D., Hughes, S.H., Arnold, E.
(2009) J Biol Chem 284: 35092

Structural basis of HIV-1 resistance to AZT by excision.
Tu, X., Das, K., Han, Q., Bauman, J.D., Clark, A.D., Hou, X., Frenkel, Y.V., Gaffney, B.L., Jones, R.A., Boyer, P.L., Hughes, S.H., Sarafianos, S.G., Arnold, E.
(2010) Nat Struct Mol Biol 17: 1202

High-resolution structures of HIV-1 reverse transcriptase/TMC278 complexes: strategic flexibility explains potency against resistance mutations.
Das, K., Bauman, J.D., Clark, A.D., Frenkel, Y.V., Lewi, P.J., Shatkin, A.J., Hughes, S.H., Arnold, E.
(2008) Proc Natl Acad Sci U S A 105: 1466

Roles of conformational and positional adaptability in structure-based design of TMC125-R165335 (etravirine) and related non-nucleoside reverse transcriptase inhibitors that are highly potent and effective against wild-type and drug-resistant HIV-1 variants.
Das, K., Clark, A.D., Lewi, P.J., Heeres, J., De Jonge, M.R., Koymans, L.M., Vinkers, H.M., Daeyaert, F., Ludovici, D.W., Kukla, M.J., De Corte, B., Kavash, R.W., Ho, C.Y., Ye, H., Lichtenstein, M.A., Andries, K., Pauwels, R., De Bethune, M.P., Boyer, P.L., Clark, P., Hughes, S.H., Janssen, P.A., Arnold, E.
(2004) J Med Chem 47: 2550

Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance.
Huang, H., Chopra, R., Verdine, G.L., Harrison, S.C.
(1998) Science 282: 1669

High resolution structures of HIV-1 RT from four RT-inhibitor complexes.
Ren, J., Esnouf, R., Garman, E., Somers, D., Ross, C., Kirby, I., Keeling, J., Darby, G., Jones, Y., Stuart, D.
(1995) Nat Struct Biol 2: 293

Organizational Affiliation:

Center for Advanced Biotechnology and Medicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA.

Macromolecules

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(by identity cutoff) | Structure

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), 3.4.23.16 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366 Go to UniProtKB: P03366
Protein Feature View Expand
Reference Sequence

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(by identity cutoff) | Structure

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), 3.4.23.16 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366 Go to UniProtKB: P03366
Protein Feature View Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff) | Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(APTPGPGPAPAPGPGPCPGPCPCPCPGPAPAPCPAPGPGPGPAPCPTPGPTP*G)-3')	E, T	27	N/A

Find similar nucleic acids by:

(by identity cutoff) | Structure

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(ACPAPGPTPCPCPCPTPGPTPTPCPGPGP(MRG)PCPGPCPCP*(ATM))-3')	F, P	21	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NVP Query on NVP Download Ideal Coordinates CCD File SDF format, chain I [A] SDF format, chain J [C] MOL2 format, chain I [A] MOL2 format, chain J [C]	A, C	11-CYCLOPROPYL-5,11-DIHYDRO-4-METHYL-6H-DIPYRIDO[3,2-B:2',3'-E][1,4]DIAZEPIN-6-ONE C₁₅ H₁₄ N₄ O NQDJXKOVJZTUJA-UHFFFAOYSA-N		Ligand Interaction