Structures of HIV-1 RT and RNA-DNA Complex Reveal a Unique RT Conformation and Substrate Interface DOI:10.2210/pdb4b3o/pdb   NDB ID: NA2190

4B3O   Display Files  close FASTA Sequence PDB File PDB File (Header) mmCIF File mmCIF File (Header) PDBML/XML File PDBML/XML File (Header)   Download Files  close FASTA Sequence PDB File (Text) PDB File (gz) mmCIF File mmCIF File (gz) PDBML/XML File PDBML/XML File (gz) Structure Factor (Text) Structure Factor (gz) Biological Assembly (gz) (A+S)   Share this Page  close Facebook Twitter LinkedIn Email Link this Page

Primary Citation       Related Citations in PDB Entry (REMARK 1) Hide     Molecular Description Hide Classification: Hydrolase/dna/rna Structure Weight: 132112.08 Molecule: REVERSE TRANSCRIPTASE/RIBONUCLEASE H Polymer: 1 Type: protein Length: 560 Chains: A EC#: 2.7.7.49    2.7.7.7    3.1.26.13    Mutation: YES Organism Human immunodeficiency virus 1 Gene Name gag-pol UniProtKB:   Protein Feature View | Search PDB | P04585     Molecule: P51 RT Polymer: 2 Type: protein Length: 441 Chains: B EC#: 2.7.7.49    2.7.7.7    3.1.26.13    Mutation: YES Organism Human immunodeficiency virus 1 Gene Name gag-pol UniProtKB:   Protein Feature View | Search PDB | P04585   Molecule: 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' Polymer: 3 Type: dna Length: 24 Chains: D Organism synthetic construct Molecule: 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' Polymer: 4 Type: rna Length: 27 Chains: R Organism synthetic construct     Source Hide Polymer: 1 Scientific Name: Human immunodeficiency virus 1   Taxonomy   Common Name: Hiv-1 Expression System: Escherichia coli   Polymer: 2 Scientific Name: Human immunodeficiency virus 1   Taxonomy   Common Name: Hiv-1 Expression System: Escherichia coli   Polymer: 3 Scientific Name: Synthetic construct (synthetic construct)   Taxonomy     Polymer: 4 Scientific Name: Synthetic construct (synthetic construct)   Taxonomy         Related PDB Entries Hide Identifier Details 1A30  HIV-1 PROTEASE COMPLEXED WITH A TRIPEPTIDE INHIBITOR  1BV7  COUNTERACTING HIV-1 PROTEASE DRUG RESISTANCE: STRUCTURAL ANALYSIS OF MUTANT PROTEASES COMPLEXED WITH XV638 AND SD146, CYCLIC UREA AMIDES WITH BROAD SPECIFICITIES  1BV9  HIV-1 PROTEASE (I84V) COMPLEXED WITH XV638 OF DUPONT PHARMACEUTICALS  1BVE  HIV-1 PROTEASE-DMP323 COMPLEX IN SOLUTION, NMR, 28 STRUCTURES  1BVG  HIV-1 PROTEASE-DMP323 COMPLEX IN SOLUTION, NMR MINIMIZED AVERAGE STRUCTURE  1BWA  HIV-1 PROTEASE (V82F/I84V) DOUBLE MUTANT COMPLEXED WITH XV638 OF DUPONT PHARMACEUTICALS  1BWB  HIV-1 PROTEASE (V82F/I84V) DOUBLE MUTANT COMPLEXED WITH SD146 OF DUPONT PHARMACEUTICALS  1C0T  CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH BM+21.1326  1C0U  CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH BM+50.0934  1C1B  CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH GCA- 186  1C1C  CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH TNK- 6123  1DMP  STRUCTURE OF HIV-1 PROTEASE COMPLEX  1DTQ  CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH PETT-1 (PETT131A94)  1DTT  CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH PETT-2 (PETT130A94)  1E6J  CRYSTAL STRUCTURE OF HIV-1 CAPSID PROTEIN (P24) IN COMPLEX WITH FAB13B5  1EP4  CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH S-1153  1ESK  SOLUTION STRUCTURE OF NCP7 FROM HIV-1  1EX4  HIV-1 INTEGRASE CATALYTIC CORE AND C-TERMINAL DOMAIN  1EXQ  CRYSTAL STRUCTURE OF THE HIV-1 INTEGRASE CATALYTIC COREDOMAIN  1FB7  CRYSTAL STRUCTURE OF AN IN VIVO HIV-1 PROTEASE MUTANT INCOMPLEX WITH SAQUINAVIR: INSIGHTS INTO THE MECHANISMS OFDRUG RESISTANCE  1FK9  CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEXWITH DMP-266(EFAVIRENZ)  1FKO  CRYSTAL STRUCTURE OF NNRTI RESISTANT K103N MUTANT HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH DMP-266(EFAVIRENZ)  1FKP  CRYSTAL STRUCTURE OF NNRTI RESISTANT K103N MUTANT HIV- 1REVERSE TRANSCRIPTASE IN COMPLEX WITH NEVIRAPINE  1G6L  1.9A CRYSTAL STRUCTURE OF TETHERED HIV-1 PROTEASE  1HIV  HIV-1 PROTEASE (HIV-1 PR) COMPLEX WITH U75875 (NOA- HIS-CHA-PSI[CH(OH)CH(OH)]VAL-ILE-APY)  1HVH  NONPEPTIDE CYCLIC CYANOGUANIDINES AS HIV PROTEASE INHIBITORS  1HVR  HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (HIV-1) PROTEASE COMPLEXED WITH XK263 OF DUPONT MERCK  1HWR  MOLECULAR RECOGNITION OF CYCLIC UREA HIV PROTEASE INHIBITORS  1HXB  HIV-1 PROTEINASE COMPLEXED WITH RO 31-8959  1JKH  CRYSTAL STRUCTURE OF Y181C MUTANT HIV-1 REVERSETRANSCRIPTASE IN COMPLEX WITH DMP-266(EFAVIRENZ)  1JLA  CRYSTAL STRUCTURE OF Y181C MUTANT HIV-1 REVERSETRANSCRIPTASE IN COMPLEX WITH TNK-651  1JLB  CRYSTAL STRUCTURE OF Y181C MUTANT HIV-1 REVERSETRANSCRIPTASE IN COMPLEX WITH NEVIRAPINE  1JLC  CRYSTAL STRUCTURE OF Y181C MUTANT HIV-1 REVERSETRANSCRIPTASE IN COMPLEX WITH PETT-2  1JLE  CRYSTAL STRUCTURE OF Y188C MUTANT HIV-1 REVERSETRANSCRIPTASE  1JLF  CRYSTAL STRUCTURE OF Y188C MUTANT HIV-1 REVERSETRANSCRIPTASE IN COMPLEX WITH NEVIRAPINE  1JLG  CRYSTAL STRUCTURE OF Y188C MUTANT HIV-1 REVERSETRANSCRIPTASE IN COMPLEX WITH UC-781  1JLQ  CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEXWITH 739W94  1KLM  HIV-1 REVERSE TRANSCRIPTASE COMPLEXED WITH BHAP U- 90152  1LV1  CRYSTAL STRUCTURE ANALYSIS OF THE NON-ACTIVE SITE MUTANT OFTETHERED HIV-1 PROTEASE TO 2.1A RESOLUTION  1LW0  CRYSTAL STRUCTURE OF T215Y MUTANT HIV-1 REVERSETRANSCRIPTASE IN COMPLEX WITH NEVIRAPINE  1LW2  CRYSTAL STRUCTURE OF T215Y MUTANT HIV-1 REVERSETRANSCRIPTASE IN COMPLEX WITH 1051U91  1LWC  CRYSTAL STRUCTURE OF M184V MUTANT HIV-1 REVERSETRANSCRIPTASE IN COMPLEX WITH NEVIRAPINE  1LWE  CRYSTAL STRUCTURE OF M41L/T215Y MUTANT HIV-1 REVERSETRANSCRIPTASE (RTMN) IN COMPLEX WITH NEVIRAPINE  1LWF  CRYSTAL STRUCTURE OF A MUTANT HIV-1 REVERSE TRANSCRIPTASE(RTMQ+M184V: M41L/D67N/K70R/M184V/T215Y) IN COMPLEX WITHNEVIRAPINE  1NCP    1O1W  SOLUTION STRUCTURE OF THE RNASE H DOMAIN OF THE HIV -1REVERSE TRANSCRIPTASE IN THE PRESENCE OF MAGNESIUM  1ODW  NATIVE HIV-1 PROTEINASE  1ODY  HIV-1 PROTEASE COMPLEXED WITH AN INHIBITOR LP-130  1QBR  HIV-1 PROTEASE INHIBITORS WIIH LOW NANOMOLAR POTENCY  1QBS  HIV-1 PROTEASE INHIBITORS WIIH LOW NANOMOLAR POTENCY  1QBT  HIV-1 PROTEASE INHIBITORS WIIH LOW NANOMOLAR POTENCY  1QBU  HIV-1 PROTEASE INHIBITORS WIIH LOW NANOMOLAR POTENCY  1REV  HIV-1 REVERSE TRANSCRIPTASE  1RT1  CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE COMPLEXED WITH MKC-442  1RT2  CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE COMPLEXED WITH TNK-651  1RT3  AZT DRUG RESISTANT HIV-1 REVERSE TRANSCRIPTASE COMPLEXED WITH 1051U91  1RT4  HIV-1 REVERSE TRANSCRIPTASE COMPLEXED WITH UC781  1RT5  HIV-1 REVERSE TRANSCRIPTASE COMPLEXED WITH UC10  1RT6  HIV-1 REVERSE TRANSCRIPTASE COMPLEXED WITH UC38  1RT7  HIV-1 REVERSE TRANSCRIPTASE COMPLEXED WITH UC84  1RTD  STRUCTURE OF A CATALYTIC COMPLEX OF HIV-1 REVERSE TRANSCRIPTASE: IMPLICATIONS FOR NUCLEOSIDE ANALOG DRUG RESISTANCE  1RTH    1RTI    1RTJ    1S1T  CRYSTAL STRUCTURE OF L100I MUTANT HIV-1 REVERSETRANSCRIPTASE IN COMPLEX WITH UC-781  1S1U  CRYSTAL STRUCTURE OF L100I MUTANT HIV-1 REVERSETRANSCRIPTASE IN COMPLEX WITH NEVIRAPINE  1S1V  CRYSTAL STRUCTURE OF L100I MUTANT HIV-1 REVERSETRANSCRIPTASE IN COMPLEX WITH TNK-651  1S1W  CRYSTAL STRUCTURE OF V106A MUTANT HIV-1 REVERSETRANSCRIPTASE IN COMPLEX WITH UC-781  1S1X  CRYSTAL STRUCTURE OF V108I MUTANT HIV-1 REVERSETRANSCRIPTASE IN COMPLEX WITH NEVIRAPINE  1T05  HIV-1 REVERSE TRANSCRIPTASE CROSSLINKED TO TEMPLATE- PRIMERWITH TENOFOVIR-DIPHOSPHATE BOUND AS THE INCOMINGNUCLEOTIDE SUBSTRATE  1TAM  HUMAN IMMUNODEFICIENCY VIRUS, NMR, MINIMIZED AVERAGE STRUCTURE  1TKT  CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEXWITH GW426318  1TKX  CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEXWITH GW490745  1TKZ  CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEXWITH GW429576  1TL1  CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEXWITH GW451211  1TL3  CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEXWITH GW450557  1VRT    1VRU    2WHH  HIV-1 PROTEASE TETHERED DIMER Q-PRODUCT COMPLEX ALONG WITH NUCLEOPHILIC WATER MOLECULE  2WOM  CRYSTAL STRUCTURE OF UK-453061 BOUND TO HIV-1 REVERSE TRANSCRIPTASE (K103N).  2WON  CRYSTAL STRUCTURE OF UK-453061 BOUND TO HIV-1 REVERSE TRANSCRIPTASE (WILD-TYPE).  3PHV  HIV-1 PROTEASE (ISOLATE HXB2)  4B37  STRUCTURES OF HIV-1 RT AND RNA-DNA COMPLEX REVEAL A UNIQUE RT CONFORMATION AND SUBSTRATE INTERFACE  4B3P  STRUCTURES OF HIV-1 RT AND RNA-DNA COMPLEX REVEAL A UNIQUE RT CONFORMATION AND SUBSTRATE INTERFACE  4B3Q  STRUCTURES OF HIV-1 RT AND RNA-DNA COMPLEX REVEAL A UNIQUE RT CONFORMATION AND SUBSTRATE INTERFACE      Ligand Chemical Component Hide Identifier Formula Name Interactions CA Search  Download  Ca CALCIUM ION   Ligand Explorer EFZ Search  Download  C14 H9 Cl F3 N O2 (-)-6-CHLORO-4-CYCLOPROPYLETHYNYL-4-TRIFLUOROMETHYL- 1,4-DIHYDRO-2H-3,1-BENZOXAZIN-2-ONE   Ligand Explorer     External Ligand Annotations Hide Identifier   Binding Affinity (Sequence Identity %) EFZ Search  Download  EC50: 4 nM (98) - data from BindingDB   IC50: 0.75 - 3400 nM (98) - data from BindingDB   Ki: 3 - 380 nM (98) - data from BindingDB   N/A in BindingMoad N/A in PDBbind     Modified Residues Hide Identifier Formula Parent Type 3DR Search  C5 H11 O6 P dnaLinking     External Domain Annotations Hide Pfam Classification: 7 Domains - data from Pfam       Structural Biology Knowledgebase Data Hide   Nucleic Acid Database Hide View the NDB ID associated with this structure: NA2190     Data in orange boxes are gathered from external resources (when available). 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Biological Assembly            View in 3D More Images... Biological assembly 1 assigned by authors and generated by PISA (software) Downloadable viewers: Simple Viewer Protein Workshop Ligand Explorer Kiosk Viewer Other Viewers  KiNG WebMol QuickPDB FirstGlance         MyPDB Personal Annotations Hide     Deposition Summary Hide Authors:   Lapkouski, M.,  Tian, L.,  Miller, J.T.,  Le Grice, S.F.J.,  Yang, W. Deposition:   2012-07-25 Release:   2013-01-16 Last Modified (REVDAT):   2013-02-20     Revision History    Hide Mouse over text for details 2013-02-20 Citation 2013-01-23 Citation     Experimental Details Hide Method:   X-RAY DIFFRACTION Exp. Data:   Structure Factors EDS   Resolution[Å]:   3.30 R-Value: 0.276 (obs.) R-Free: 0.295 Space Group: P 31 2 1 Unit Cell:   Length [Å] Angles [°] a = 164.60 α = 90.00  b = 164.60 β = 90.00  c = 129.03 γ = 120.00      Molecule of the Month Hide Reverse Transcriptase