Primary Citation PubMed: 9831551
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SplitTester: software to identify domains responsible for functional divergence in protein family.
(2005) BMC Bioinformatics 6
PubMed: 15929795 | PubMedCentral: PMC1181622 | DOI: 10.1186/1471-2105-6-137
(B) The X-ray structure of the HIV reverse transcriptase/primer/template complex (1RTD).
Publication Year: 2005
Nucleotide modification at the gamma-phosphate leads to the improved fidelity of HIV-1 reverse transcriptase.
(2005) Nucleic Acids Res 33
PubMed: 16141194 | PubMedCentral: PMC1197130 | DOI: 10.1093/nar/gki779
was employed (PDB code: 1RTD) ( 30 ).
Why do HIV-1 and HIV-2 use different pathways to develop AZT resistance?
(2006) PLoS Pathog 2
PubMed: 16485036 | PubMedCentral: PMC1364504 | DOI: 10.1371/journal.ppat.0020010
As has already been discussed, HIV-2 RT is a fully competent polymerase and carries out pyrophosphate-mediated excision with an efficiency similar to HIV-1 RT. Figure 7 Position of the Side Chain of A... ino Acid Residue K219 in HIV-1 RT and K220 in HIV-2 RT Unliganded HIV-2 RT (shown in magenta; PDB code 1MU2) and HIV-1 RT/DNA/dTTP (shown in white with the dTTP and DNA omitted for clarity; PDB code 1RTD), is superimposed on the Cα protein backbone of HIV-1 RT/DNA/tenofovir-diphosphate (shown in cyan; PDB code 1TO5).
Figure 8 Superposition of HIV-1 RT and HIV-2 RT Showing the Possible Effects of a Phe116Tyr Mutation Unliganded HIV-2 RT (PDB code 1MU2) is shown in yellow, unliganded HIV-1RT (PDB code 1DLO) is shown in cyan, and HIV-1 RT/DNA/dTTP (PDB code 1RTD) is shown in red.
Publication Year: 2006
Specific binding of a hexanucleotide to HIV-1 reverse transcriptase: a novel class of bioactive molecules.
(2006) Nucleic Acids Res 34
PubMed: 17038335 | PubMedCentral: PMC1635251 | DOI: 10.1093/nar/gkl533
Modeling and docking studies Rigid-body docking studies of HIV-1 RT (Brookhaven Protein Data Bank accession nos: 1HMV, 1RTH, 1RTD and 1HVU) and Hex-S3 were performed with the program Hex 4.2 ( 15 ).
Polymerase-catalyzed synthesis of DNA from phosphoramidate conjugates of deoxynucleotides and amino acids.
(2007) Nucleic Acids Res 35
PubMed: 17652326 | PubMedCentral: PMC1976459 | DOI: 10.1093/nar/gkm498
Model building The modelling is based on the crystal structure of RT in complex with a trapped entering triphosphate (pdb structure file 1RTD) ( 51 ).
Publication Year: 2007
Active site binding and sequence requirements for inhibition of HIV-1 reverse transcriptase by the RT1 family of single-stranded DNA aptamers.
PubMed: 17644816 | PubMedCentral: PMC1976467 | DOI: 10.1093/nar/gkm420
Overlaying these sites with a crystal structure of HIV-1 RT bound to a dsDNA primer-template [2HMI and 1RTD, ( 30 , 34 )] show this difference in intensities can be explained by the formation of a dou... le helix and that these regions would be solvent exposed if they bound RT as primer-template mimics ( Figure 9 A).
RT1t49 was modeled onto the primer-template binding complex bound to HIV-RT [HMI and 1RTD, ( 30 , 34 )].
Utilization of a deoxynucleoside diphosphate substrate by HIV reverse transcriptase.
(2008) PLoS One 3
PubMed: 18446195 | PubMedCentral: PMC2312326 | DOI: 10.1371/journal.pone.0002074
Figures were generated from the published HIV-1 RT ternary structure (1rtd)  using the UCSF Chimera package  .
Publication Year: 2008
Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes.
(2008) PLoS Comput Biol 4
PubMed: 18989394 | PubMedCentral: PMC2566816 | DOI: 10.1371/journal.pcbi.1000214
Thus, the following structures were used: Gag derived proteins: matrix p17, capsid p24, nucleocapsid p7 (PDB IDs: 1tam, 1e6j, 1a1t, respectively); Pol derived proteins: protease p10, reverse transcrip... ase p51, RNase p15, integrase p31 (PDB IDs: 1aaq, 1rtd, 1o1w, 2itg, respectively); Vpr p12/p10 (PDB ID: 1m8l); Tat p16/p14 (PDB ID: 1mnb); Rev p19 (PDB ID: 1etf); Vpu p16 (PDB ID: 1vpu); Env derived proteins: gp120, gp41 (PDB IDs: 1gc1, 1env, respectively); Nef p27/p25 (PDB ID: 2nef).
For the RT protein (Protein Data Bank (PDB)  ID 1rtd): 15 of 416 surface sites and only one out of 138 buried sites were found to be rate-shifting (the sites are detailed in Table S1 ).
Interactions between HIV-1 reverse transcriptase and the downstream template strand in stable complexes with primer-template.
PubMed: 18974785 | PubMedCentral: PMC2570493 | DOI: 10.1371/journal.pone.0003561
Three residues of the downstream template overhang are resolved in the crystal structure of the +1 dNTP•RT•P/T ternary complex (PDB databank, 1RTD)  .
28]; however, the path of the template extension differs in this structure from that in the 1RTD structure.
Nucleic acid polymerases use a general acid for nucleotidyl transfer.
(2009) Nat Struct Mol Biol 16
PubMed: 19151724 | PubMedCentral: PMC2728625 | DOI: 10.1038/nsmb.1540
R/DdDp (RT): HIV RT with TTP bound to the active site in the presence of two Mg 2+ ions (pdb 1RTD) 14 .
Publication Year: 2009
HIV reverse transcriptase: structural interpretation of drug resistant genetic variants from India.
(2010) Bioinformation 4
PubMed: 20011151 | PubMedCentral: PMC2770369 | DOI: null
The protein databank codes of the crystal structures of bound and unbound forms of RT used in this study are 1IKW [ 6 ], 1VRT [ 7 ], 1DLO [ 8 ], 1HMV [ 9 ], 1RTJ [ 10 ] and 1RTD [ 11 ].
In the template/primer bound RT structure (1RTD), Lys 101 side chain makes van der Waals contacts with the side chain of Tyr 319 ( Figure 1D ).
(B-F) Local hydrogen bond interactions involving K101 in unliganded RT structure 1DLO,1HMV,1RTD, 1RTJ and in Nevirapine bound RT 1VRT (G) Structural superposition of 1IKW (yellow) and 1RTJ (green) showing changes in residue conformations.
Publication Year: 2010
Allosteric regulation of HIV-1 reverse transcriptase by ATP for nucleotide selection.
(2010) PLoS One 5
PubMed: 20111609 | PubMedCentral: PMC2810339 | DOI: 10.1371/journal.pone.0008867
We used two crystal structures of the HIV-1 RTs (PDB code: 1N6Q  and 1RTD  ) as modeling templates.
Mechanistic characterization and molecular modeling of hepatitis B virus polymerase resistance to entecavir.
PubMed: 20169198 | PubMedCentral: PMC2820545 | DOI: 10.1371/journal.pone.0009195
Homology Models of HBV-RT/DNA Complex A homology model for the wildtype HBV-RT/DNA/dGTP complex was developed based on the sequence alignment between HBV RT and HIV RT  and the HIV... RT/DNA x-ray structure (1RTD.
Structural Aspects of Drug Resistance and Inhibition of HIV-1 Reverse Transcriptase.
(2010) Viruses 2
PubMed: 20376302 | PubMedCentral: PMC2850067 | DOI: 10.3390/v2020606
The software Coot [ 55 ] was used to prepare various sugar ring conformations of the primer terminus and incoming dNTP, starting from the structural coordinates of the HIV-1 RT/DNA/dNTP ternary comple... (PDB Code 1rtd).
Due to lack of the primer 3′OH group in the crystal structure (PDB file 1rtd), the coordination of metal ion A (known as catalytic metal) is incomplete.
The Role of Nucleotide Excision by Reverse Transcriptase in HIV Drug Resistance.
PubMed: 20523911 | PubMedCentral: PMC2879589 | DOI: 10.3390/v2020372
(B) Ternary complex of HIV-1 RT with ddAMP-terminated primer-template and dTTP occupying the N site [PDB structure 1RTD, Ref.
Computational Analysis of Molecular Interaction Networks Underlying Change of HIV-1 Resistance to Selected Reverse Transcriptase Inhibitors.
(2010) Bioinform Biol Insights 4
PubMed: 21234299 | PubMedCentral: PMC3020081 | DOI: 10.4137/BBI.S6247
(PDB structure: 1RTD).
Distances (in Å) between alpha-carbon atoms were calculated from PDB: 1RTD structure, chain A. Acknowledgement Funding The presented research has been partially supported by the Knut and Alice Wallenberg Foundation, by the Swedish Foundation for Strategic Research and by grant nr.
Mutation rates and intrinsic fidelity of retroviral reverse transcriptases.
(2009) Viruses 1
PubMed: 21994586 | PubMedCentral: PMC3185545 | DOI: 10.3390/v1031137
Atomic coordinates were taken from Protein Data Bank file 1RTD [ 114 ].
HIV-1 Ribonuclease H: Structure, Catalytic Mechanism and Inhibitors.
PubMed: 21994660 | PubMedCentral: PMC3185654 | DOI: 10.3390/v2040900
A Crystal structure of HIV-1 RT (PDB code: 1RTD.
B Crystal structures of the RNase H domain of HIV-1 RT (PDB code:1RTD) [ 5 ], human RNase H1 (PDB code: 2QKB) [ 12 ] and E. coli RNase H1 (PBD code: 1WSJ).
Substrate mimicry: HIV-1 reverse transcriptase recognizes 6-modified-3'-azido-2',3'-dideoxyguanosine-5'-triphosphates as adenosine analogs.
(2012) Nucleic Acids Res 40
PubMed: 21914723 | PubMedCentral: PMC3245946 | DOI: 10.1093/nar/gkr756
Each of the analogs was modeled into the ternary RT-T/P-TTP complex (pdb co-ordinates 1RTD).
Publication Year: 2012
Molecular dynamics simulation in virus research.
(2012) Front Microbiol 3
PubMed: 22833741 | PubMedCentral: PMC3400276 | DOI: 10.3389/fmicb.2012.00258
The structures of HIV-1 PR (PDB code: 1HHP), HIV-1 RT (PDB code: 1RTD), STMV (PDB code: 1A34), and poliovirus capsid particle (PDB code: 1HXS), which are deposited in the Protein Data Bank (PDB) ( htt... ://www.rcsb.org/pdb/home/home.do ) or the VIPERdb ( http://viperdb.scripps.edu/ ), are shown in surface representation.
Highly similar structural frames link the template tunnel and NTP entry tunnel to the exterior surface in RNA-dependent RNA polymerases.
(2013) Nucleic Acids Res 41
PubMed: 23275546 | PubMedCentral: PMC3561941 | DOI: 10.1093/nar/gks1251
Viral species and PDB structures used as queries in this study Queries Abbreviations PDB Length of structure Picornaviridae, RdRp, +ssRNA Poliovirus PV 1RA6 ( 3 ) 4... 1 Poliovirus (open) PV 3OL6 ( 9 ) 471 Poliovirus (closed) PV 3OL7 ( 9 ) 471 Coxsackie virus COXV 3DDK ( 11 ) 462 Human rhinovirus HRV 1XR6 ( 12 ) 460 Human rhinovirus HRV 1XR7 ( 12 ) 460 Foot and mouth disease virus FMDV 1U09 ( 2 ) 476 Caliciviridae, RdRp, +ssRNA Norwalk virus NV 1SH0 ( 13 ) 510 Rabbit hemorrhagic disease virus RHDV 1KHV ( 14 ) 516 Rabbit hemorrhagic disease virus RHDV 1KHW ( 14 ) 516 Sapporo virus SAPV 2CKW ( 15 ) 515 Flaviviridae, RdRp, +ssRNA Hepatitis C virus HCV 1NB4 ( 16 ) 570 Hepatitis C virus HCV 1NB7 ( 16 ) 570 Bovine viral diarrhea virus BVDV 1S48 ( 17 ) 609 West Nile (Kunjin) virus WNV 2HCS ( 18 ) 595 Dengue virus DENV 2J7U ( 19 ) 635 Cystoviridae, RdRp, dsRNA Bacteriophage Phi6 PHI6 1HHS ( 20 ) 664 Bacteriophage Phi6 PHI6 1HI0 ( 20 ) 664 Reoviridae, RdRp, dsRNA Reovirus lambda 3 REOV 1MUK ( 21 ) 1267 Reovirus lambda 3 REOV 1N35 ( 21 ) 1267 Rotavirus ROTAV 2R7X ( 22 ) 1095 Birnaviridae, RdRp, dsRNA Infectious bursal disease, birnavirus IBDV 2PGG ( 5 ) 774 Infectious pancreatic necrosis IPNV 2YI8 ( 23 ) 799 Infectious pancreatic necrosis IPNV 2YI9 ( 23 ) 799 Infectious pancreatic necrosis IPNV 2YIA ( 23 ) 799 RdDp HIV1 HIV1 1RT1 ( 24 ) 560 HIV1 (closed) HIV1 1RTD ( 25 ) 554 HIV1 (open) HIV1 2HMI ( 26 ) 558 Tribolium castaneum TERT 3DU6 ( 27 ) 596 DdRp Bacteriophage T7 (closed) T7 RNAP 1S77 ( 28 ) 883 Bacteriophage T7 (closed) T7 RNAP 2AJQ ( 29 ) 704 Bacteriophage T7 (open) T7 RNAP 1MSW ( 30 ) 883 Bacteriophage N4 N4 3C2P ( 31 ) 1117 DdDp Thermus aquaticus (open) TAQ 2KTQ ( 32 ) 538 Thermus aquaticus (closed) TAQ 3KTQ ( 32 ) 540 Thermus aquaticus (open) TAQ 4KTQ ( 32 ) 539 Bacteriophage T7 T7 DNAP 1T7P ( 33 ) 698 Queries of both open and closed structures were used to assess the impact of this feature on R2R correspondence.
Publication Year: 2013
Impact of rtI233V mutation in hepatitis B virus polymerase protein and adefovir efficacy: Homology modeling and molecular docking studies.
(2013) Bioinformation 9
PubMed: 23423477 | PubMedCentral: PMC3569598 | DOI: 10.6026/97320630009121
Molecular docking studies : To the modelled protein, the two magnesium (Mg 2+ ) ions and the template primer DNA duplex [d (GCXCCGGCGCTC)- d(GAGCGCCGG)] were located based on the co-ordinates of PDB: ... RTD chain A of HIV-1rt.
The query coverage (39% and 58% respectively) and identity score (E value: 0.009 and 0.022 respectively) for these templates were good when compared to previously described template of HIV-1rt [PDB: 1RTD A (query coverage 22% and E value 0.75)].
The two magnesium (Mg 2+ ) ions, thymidine triphoshate and the DNA template were located using the coordinates of PDB: 1RTD A of HIV-1rt.
The three dimensional model of HBV polymerase/rt was constructed using the HIV-1rt template (PDB code: 1RTD A) and the model was evaluated by the Ramachandran plot.
Homology model of hepatitis B virus polymerase/rt : Homology model of HBVrt was built in MODELLER 9v8 using the crystal structure of HIV-1rt template [Protein Data Bank (PDB) code: 1RTD chain A].
Structural analysis of monomeric retroviral reverse transcriptase in complex with an RNA/DNA hybrid.
PubMed: 23382176 | PubMedCentral: PMC3616737 | DOI: 10.1093/nar/gkt053
( B and D ) Superposition of the palm/fingers subdomain from XMRV RT complex structure, HIV-1 RT in complex with RNA/DNA (PDB ID: 1HYS) (B) and HIV-1 RT complexed with dsDNA (PDB: 1RTD) (D).
These superimpose well between XMRV RT – substrate complex and HIV-1 ternary complex (PDB ID: 1RTD), adopting a ‘half-open’ conformation ( 11 ), whereas the conformation in the HIV-1 RT – RNA/DNA complex (PDB ID: 1HYS) is more open ( Figure 4 B and D).
( C and E ) palm subdomain-based superposition of XMRV RT complex structure with structures of HIV-1 RT complexed with RNA/DNA (PDB ID: 1HYS) (E) and dsDNA (PDB ID: 1RTD) (C).
Tyr64 and residues forming the ‘pin’ stabilizing the conformation of the template in front of the incoming nucleotide are shown as cyan sticks, and the dNTP modelled based on the HIV-1 RT structure (PDB ID: 1RTD) is shown as dark grey sticks.
Comparison with structures of HIV-1 RT We compared the structures of XMRV RT and HIV-1 RT containing (i) an RNA/DNA (PDB ID: 1HYS) ( 12 ) and (ii) dsDNA and the incoming nucleotide (PDB ID: 1RTD) ( 11 ).
Superpositions of the structures of substrate-bound XMRV and HIV-1 RTs Superimposed domain (Total number of traced Cα atoms in each XMRV RT domain given in parentheses) RMSD (Å) calculated for: Substrate Fingers Palm Thumb Connection RNA/DNA complex, 1HYS Substrate 30 pairs of atoms a 0.5 5.8 2.3 3.1 4.1 Fingers 84 pairs of Cα atoms (of 106) 7.3 1.7 8.2 14.9 17.1 Palm 91 pairs of Cα atoms (of 136) 1.1 4.6 1.3 3.1 3.1 Thumb 53 pairs of Cα atoms (of 79) 2.9 6.1 5.3 1.6 2.3 Connection 54 pairs of Cα atoms (of 120) 4.7 8.1 5.7 3.1 1.6 dsDNA complex, 1RTD Substrate 24 pairs of atoms a 0.4 2.4 1.8 3.0 3.4 Fingers 84 pairs of Cα atoms (of 106) 1.6 1.2 3.6 3.7 6.2 Palm 91 pairs of Cα atoms (of 136) 0.7 2.7 1.3 3.0 3.2 Thumb 53 pairs of Cα atoms (of 79) 2.7 3.5 4.4 1.5 2.8 Connection 54 pairs of Cα atoms (of 120) 5.2 7.3 5.8 3.1 1.6 The individual subdomains were superimposed [the resulting root mean square deviations (RMSDs) of pairs of C−α atoms are shown in bold] and the RMSD values for the other subdomains are given.
The palm, thumb and connection subdomains of XMRV RT (198 C-α atoms) can be superimposed on structures of HIV-1 RT with an RMSD of 2.0 and 1.9 Å for 1HYS and 1RTD, respectively.
Inhibitors of HIV-1 Reverse Transcriptase-Associated Ribonuclease H Activity.
(2012) Biology (Basel) 1
PubMed: 23599900 | PubMedCentral: PMC3627382 | DOI: 10.3390/biology1030521
The figure is derived from PDB file 1RTD and was drawn using UCSF Chimera software [ 6 ].
Altered error specificity of RNase H-deficient HIV-1 reverse transcriptases during DNA-dependent DNA synthesis.
PubMed: 23444139 | PubMedCentral: PMC3632107 | DOI: 10.1093/nar/gkt109
( A ) Ternary complex of HIV-1 group M subtype B RT, double-stranded DNA and dTTP [PDB coordinates from Huang et al. ( 39 ), PDB code 1RTD].
Computational simulation strategies for analysis of multisubunit RNA polymerases.
(2013) Chem Rev 113
PubMed: 23987500 | PubMedCentral: PMC3829680 | DOI: 10.1021/cr400046x
A combined MD QM/MM simulation based on the crystal structure (PDB ID 1RTD) was carried out with a focus on the donor of the second proton, as Castro et al. 38a indicated that a Lys was the responsibl... acid in HIV-RT.
Variation of human immunodeficiency virus type-1 reverse transcriptase within the simian immunodeficiency virus genome of RT-SHIV.
(2014) PLoS One 9
PubMed: 24498008 | PubMedCentral: PMC3909041 | DOI: 10.1371/journal.pone.0086997
In order to generate Figure 1 , the X-ray crystal structure coordinates for a wild type HIV-1 RT ternary complex containing DNA primer/template and an incoming nucleotide were downloaded from the Prot... in Data Bank (PDB) at www.pdb.org  (PDB ID:1RTD  ).
The X-ray crystal structure PDB ID: 1RTD  of pre-catalytic, wild type HIV-1 reverse transcriptase in complex with double stranded DNA and incoming nucleotide was used to make the image.
Publication Year: 2014
Complexes of HIV-1 RT, NNRTI and RNA/DNA hybrid reveal a structure compatible with RNA degradation.
(2013) Nat Struct Mol Biol 20
PubMed: 23314251 | PubMedCentral: PMC3973182 | DOI: 10.1038/nsmb.2485
( c ) The ternary complex structure 1RTD 26 representing all previously reported RT–DNA complexes.
( a ) Pairwise comparisons of RT in the 3V81 structure with RT complexed with Nevirapine (3QIP 14 ), an RT ternary complex (1RTD 26 ), and our WT22Efv (4B3O).
Structures were solved by molecular replacement using the RT from the ternary complex (1RTD) and RT with NNRTI (1FK9) 22 , 26 with MolRep in CCP4 56 .
Biophysical Insights into the Inhibitory Mechanism of Non-Nucleoside HIV-1 Reverse Transcriptase Inhibitors.
(2013) Biomolecules 3
PubMed: 24970195 | PubMedCentral: PMC4030976 | DOI: 10.3390/biom3040889
RT is pictured as a solvent-accessible surface area model (taken from PDB ID: 1RTD).
Drug resistance in non-B subtype HIV-1: impact of HIV-1 reverse transcriptase inhibitors.
(2014) Viruses 6
PubMed: 25254383 | PubMedCentral: PMC4189038 | DOI: 10.3390/v6093535
The backbone of HIV-1 RT (PDB file 1RTD) [ 21 ] is shown in light gray ribbon representation.
PubMed ID is not available.
Published in 2014
Accelerated molecular dynamics simulations of PIFE Accelerated molecular dynamics (AMD) simulations were performed on the atomic coordinates of the ternary RT-T/P-dTTP complex (PDB: 1RTD) ( 20 ) modif... ed at the 5′-end of the primer with Cy3 and included harmonic constraints on all Cα and P atoms not within 25 Å of Cy3.
Current perspectives on HIV-1 antiretroviral drug resistance.
PubMed: 25341668 | PubMedCentral: PMC4213579 | DOI: 10.3390/v6104095
PDB 1RTD [ 94 ].
Published in 2015
The color-coding is as in Figure 1 b; ( b ) A structure-based sequence alignment depicting the conservation of RdRP motifs (pdb entries: 4K6M, 1S4F, 1NB4, 3OL6, 3BSO, 3AVT [ 36 ], 1HI0, 2PGG [ 37 ], 4... RT [ 38 ], 1RTD [ 39 ], and 3DU6 [ 40 ]).
Publication Year: 2015
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