+Open data
-Basic information
Entry | Database: PDB / ID: 6uit | ||||||
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Title | HIV-1 wild-type reverse transcriptase-DNA complex with dCTP | ||||||
Components |
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Keywords | VIRAL PROTEIN / HIV-1 reverse transcriptase NRTI polymerase DNA complex | ||||||
Function / homology | Function and homology information integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / : / : / Assembly Of The HIV Virion / HIV-1 retropepsin / retroviral ribonuclease H / Budding and maturation of HIV virion / exoribonuclease H / exoribonuclease H activity / protein processing / host multivesicular body / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / peptidase activity / viral nucleocapsid / symbiont-mediated suppression of host gene expression / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / DNA binding / RNA binding / zinc ion binding / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 1 group M subtype B Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.80607409399 Å | ||||||
Authors | Lansdon, E.B. | ||||||
Citation | Journal: Commun Biol / Year: 2019 Title: Elucidating molecular interactions ofL-nucleotides with HIV-1 reverse transcriptase and mechanism of M184V-caused drug resistance. Authors: Hung, M. / Tokarsky, E.J. / Lagpacan, L. / Zhang, L. / Suo, Z. / Lansdon, E.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6uit.cif.gz | 237.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6uit.ent.gz | 178.1 KB | Display | PDB format |
PDBx/mmJSON format | 6uit.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ui/6uit ftp://data.pdbj.org/pub/pdb/validation_reports/ui/6uit | HTTPS FTP |
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-Related structure data
Related structure data | 6uirC 6uisC 6ujxC 6ujyC 6ujzC 6uk0C 3kk1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 65887.328 Da / Num. of mol.: 1 / Mutation: Q845C, C867S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate HXB2) Strain: isolate HXB2 / Gene: gag-pol / Production host: Escherichia coli (E. coli) References: UniProt: P04585, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H |
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#2: Protein | Mass: 51382.984 Da / Num. of mol.: 1 / Mutation: C867S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate HXB2) Strain: isolate HXB2 / Gene: gag-pol / Production host: Escherichia coli (E. coli) References: UniProt: P04585, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H |
-DNA chain , 2 types, 2 molecules PT
#3: DNA chain | Mass: 6360.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 |
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#4: DNA chain | Mass: 8448.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 |
-Non-polymers , 4 types, 39 molecules
#5: Chemical | ChemComp-DCP / | ||||
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#6: Chemical | #7: Chemical | ChemComp-MG / | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 2% PEG 4000, 100mM MES pH 6, 10mM magnesium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97395 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97395 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 35132 / % possible obs: 99.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 44.4190214794 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 2.8→2.85 Å / Rmerge(I) obs: 0.627 / Num. unique obs: 3187 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3kk1 Resolution: 2.80607409399→47.0947679253 Å / SU ML: 0.339743359189 / Cross valid method: THROUGHOUT / σ(F): 1.33597051911 / Phase error: 27.8207043683
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.5978548237 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.80607409399→47.0947679253 Å
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Refine LS restraints |
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LS refinement shell |
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