ISDA

Deposition Date 2011-12-22

Release Date 2012-01-18

Last Version Date 2024-11-20

Entry Detail

PDB ID:

3V81

Keywords:

TRANSFERASE/DNA

Title:

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

Biological Source:

Source Organism:

Human immunodeficiency virus type 1 BH10 (Taxon ID: 11678)
(Taxon ID: )

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.85 Å

R-Value Free:

0.29

R-Value Work:

0.25

R-Value Observed:

0.25

Space Group:

P 1 21 1

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:HIV-1 Reverse Transcriptase P66 subunit
Gene (Uniprot):gag-pol
Mutations:Q258C, C280S, D498N
Chain IDs:A, C
Chain Length:556
Number of Molecules:2
Biological Source:Human immunodeficiency virus type 1 BH10

UniProt ID:P03366 Pfam ID:PF00078, PF06817, PF06815, PF00075 EC:3.1.26.13

Protein Blast

Polymer Type:polypeptide(L)
Molecule:HIV-1 Reverse Transcriptase P51 subunit
Gene (Uniprot):gag-pol
Chain IDs:B, D
Chain Length:428
Number of Molecules:2
Biological Source:Human immunodeficiency virus type 1 BH10

UniProt ID:P03366 Pfam ID:PF00078, PF06817, PF06815, PF00075 EC:3.1.26.13

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(ATM))-3')
Chain IDs:F (auth: P), H (auth: F)
Chain Length:21
Number of Molecules:2
Biological Source:

Polymer Type:polydeoxyribonucleotide
Molecule: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')
Chain IDs:E (auth: T), G (auth: E)
Chain Length:27
Number of Molecules:2
Biological Source:

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
ATM	F	DT	?
MRG	F	DG	?

Ligand Molecules

NVP

Primary Citation

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

Das, K, Martinez, S.E, Bauman, J.D, Arnold, E, 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, 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, Das, K, Bauman, J.D, Clark, A.D, Frenkel, Y.V, Lewi, P.J, Shatkin, A.J, Hughes, S.H, Arnold, E, 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, Huang, H, Chopra, R, Verdine, G.L, Harrison, S.C, Ren, J, Esnouf, R, Garman, E, Somers, D, Ross, C, Kirby, I, Keeling, J, Darby, G, Jones, Y, Stuart, D.Show

Nat.Struct.Mol.Biol. 19 253 259 (2012)

PMID: 22266819 DOI: 10.1038/nsmb.2223

Abstact

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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Primary Citation of related structures