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Yorodumi- PDB-3kk2: HIV-1 reverse transcriptase-DNA complex with dATP bound in the nu... -
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-Basic information
Entry | Database: PDB / ID: 3kk2 | ||||||
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Title | HIV-1 reverse transcriptase-DNA complex with dATP bound in the nucleotide binding site | ||||||
Components |
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Keywords | TRANSFERASE/DNA / HIV / reverse transcriptase / protein-DNA complex / TRANSFERASE-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 / 2-LTR circle formation / Uncoating of the HIV Virion / 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 / 2-LTR circle formation / Uncoating of the HIV Virion / 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 / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / Assembly Of The HIV Virion / retroviral ribonuclease H / exoribonuclease H / Budding and maturation of HIV virion / exoribonuclease H activity / protein processing / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / peptidase activity / viral nucleocapsid / aspartic-type endopeptidase activity / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / DNA binding / zinc ion binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Lansdon, E.B. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Visualizing the molecular interactions of a nucleotide analog, GS-9148, with HIV-1 reverse transcriptase-DNA complex. Authors: Lansdon, E.B. / Samuel, D. / Lagpacan, L. / Brendza, K.M. / White, K.L. / Hung, M. / Liu, X. / Boojamra, C.G. / Mackman, R.L. / Cihlar, T. / Ray, A.S. / McGrath, M.E. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kk2.cif.gz | 237.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kk2.ent.gz | 184.1 KB | Display | PDB format |
PDBx/mmJSON format | 3kk2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kk2_validation.pdf.gz | 818.1 KB | Display | wwPDB validaton report |
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Full document | 3kk2_full_validation.pdf.gz | 858.1 KB | Display | |
Data in XML | 3kk2_validation.xml.gz | 41.4 KB | Display | |
Data in CIF | 3kk2_validation.cif.gz | 56.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kk/3kk2 ftp://data.pdbj.org/pub/pdb/validation_reports/kk/3kk2 | HTTPS FTP |
-Related structure data
Related structure data | 3kjvSC 3kk1C 3kk3C 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
-Reverse transcriptase ... , 2 types, 2 molecules AB
#1: Protein | Mass: 64521.895 Da / Num. of mol.: 1 / Mutation: C280S, Q258C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: HXB2D / Gene: gag-pol / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P04585, RNA-directed DNA polymerase |
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#2: Protein | Mass: 52748.418 Da / Num. of mol.: 1 / Mutation: C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: HXB2D / Gene: gag-pol / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P04585, RNA-directed DNA polymerase |
-DNA chain , 2 types, 2 molecules PT
#3: DNA chain | Mass: 6360.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: primer DNA |
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#4: DNA chain | Mass: 8423.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: template DNA |
-Non-polymers , 4 types, 92 molecules
#5: Chemical | #6: Chemical | #7: Chemical | ChemComp-DTP / | #8: Water | ChemComp-HOH / | |
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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: 2.74 Å3/Da / Density % sol: 55.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 3% PEG4000, 0.05M MES pH 6.0, 5mM magnesium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 2, 2008 |
Radiation | Monochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 33944 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 2.9 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.9→2.96 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 3.4 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KJV Resolution: 2.9→29.77 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 34311.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.3952 Å2 / ksol: 0.314152 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→29.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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