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Yorodumi- PDB-5j2m: HIV-1 reverse transcriptase in complex with DNA and EFdA-triphosp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5j2m | ||||||||||||||||||||||||
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Title | HIV-1 reverse transcriptase in complex with DNA and EFdA-triphosphate, a translocation-defective RT inhibitor | ||||||||||||||||||||||||
Components |
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Keywords | transferase/dna / HIV-1 / reverse transcriptase / RT / DNA / double stranded DNA / dsDNA / EFdA / 4'-ethynyl-2-fluoro-2'-deoxyadenosine / EFdA-triphosphate / EFdA-TP / inhibitors / NRTI / TDRTI / translocation defective / 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 / Early Phase of HIV Life Cycle / Vpr-mediated nuclear import of PICs / 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 / Early Phase of HIV Life Cycle / Vpr-mediated nuclear import of PICs / 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 / host multivesicular body / protein processing / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / peptidase activity / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / viral translational frameshifting / 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 group M subtype B Human immunodeficiency virus 1 | ||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.432 Å | ||||||||||||||||||||||||
Authors | Salie, Z.L. / Kirby, K.A. / Sarafianos, S.G. | ||||||||||||||||||||||||
Funding support | United States, 7items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Structural basis of HIV inhibition by translocation-defective RT inhibitor 4'-ethynyl-2-fluoro-2'-deoxyadenosine (EFdA). Authors: Salie, Z.L. / Kirby, K.A. / Michailidis, E. / Marchand, B. / Singh, K. / Rohan, L.C. / Kodama, E.N. / Mitsuya, H. / Parniak, M.A. / Sarafianos, S.G. | ||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5j2m.cif.gz | 244 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j2m.ent.gz | 188.4 KB | Display | PDB format |
PDBx/mmJSON format | 5j2m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5j2m_validation.pdf.gz | 804.7 KB | Display | wwPDB validaton report |
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Full document | 5j2m_full_validation.pdf.gz | 810.2 KB | Display | |
Data in XML | 5j2m_validation.xml.gz | 39.6 KB | Display | |
Data in CIF | 5j2m_validation.cif.gz | 56 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j2/5j2m ftp://data.pdbj.org/pub/pdb/validation_reports/j2/5j2m | HTTPS FTP |
-Related structure data
Related structure data | 5j2nC 5j2pC 5j2qC 3kk1S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-HIV-1 reverse transcriptase p51 ... , 2 types, 2 molecules AB
#1: Protein | Mass: 64521.895 Da / Num. of mol.: 1 / Fragment: unp residues 1-560 / Mutation: Q258C, C280S 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 / Plasmid: pCDFDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL References: UniProt: P04585, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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#2: Protein | Mass: 51382.984 Da / Num. of mol.: 1 / Fragment: unp residues 1-440 / Mutation: C280S 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 / Plasmid: pRSFDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL References: UniProt: P04585, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
-DNA chain , 2 types, 2 molecules PT
#3: DNA chain | Mass: 6490.267 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 |
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#4: DNA chain | Mass: 8383.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 |
-Non-polymers , 3 types, 388 molecules
#5: Chemical | #6: Chemical | ChemComp-6FN / | #7: 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: 2.8 Å3/Da / Density % sol: 56.14 % |
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Crystal grow | Temperature: 291.1 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 8% PEG4000, 25mM MES pH 6.0, 5mM magnesium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Jul 30, 2014 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.432→65.23 Å / Num. obs: 54563 / % possible obs: 99.5 % / Redundancy: 7.4 % / Biso Wilson estimate: 44.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.031 / Rrim(I) all: 0.086 / Net I/σ(I): 19.8 / Num. measured all: 402756 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KK1 Resolution: 2.432→65.231 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.37 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 151.76 Å2 / Biso mean: 50.9125 Å2 / Biso min: 16.93 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.432→65.231 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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