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Yorodumi- PDB-3klh: Crystal structure of AZT-Resistant HIV-1 Reverse Transcriptase cr... -
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-Basic information
Entry | Database: PDB / ID: 3klh | ||||||
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Title | Crystal structure of AZT-Resistant HIV-1 Reverse Transcriptase crosslinked to post-translocation AZTMP-Terminated DNA (COMPLEX P) | ||||||
Components |
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Keywords | TRANSFERASE/DNA / HIV-1 / REVERSE TRANSCRIPTASE / RT / AZT / AZT EXCISION / AZT RESISTANCE / RESISTANCE MECHANISM / AZT RESISTANCE MUTATIONS / P51/P66 / NUCLEOSIDE INHIBITOR / AIDS / HIV / DNA POLYMERASE / NRTI / NUCLEOTIDE EXCISION / DNA-DIRECTED DNA POLYMERASE / MAGNESIUM / METAL-BINDING / MULTIFUNCTIONAL ENZYME / NUCLEASE / RNA-DIRECTED DNA POLYMERASE / TRANSFERASE / TRANSFERASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / 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 / 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 / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 1 MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Tu, X. / Sarafianos, S.G. / Arnold, E. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2010 Title: Structural basis of HIV-1 resistance to AZT by excision. Authors: Tu, X. / Das, K. / Han, Q. / Bauman, J.D. / Clark, A.D. / Hou, X. / Frenkel, Y.V. / Gaffney, B.L. / Jones, R.A. / Boyer, P.L. / Hughes, S.H. / Sarafianos, S.G. / Arnold, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3klh.cif.gz | 327.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3klh.ent.gz | 255.1 KB | Display | PDB format |
PDBx/mmJSON format | 3klh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3klh_validation.pdf.gz | 490.3 KB | Display | wwPDB validaton report |
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Full document | 3klh_full_validation.pdf.gz | 555.4 KB | Display | |
Data in XML | 3klh_validation.xml.gz | 59.9 KB | Display | |
Data in CIF | 3klh_validation.cif.gz | 82.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kl/3klh ftp://data.pdbj.org/pub/pdb/validation_reports/kl/3klh | HTTPS FTP |
-Related structure data
Related structure data | 3kleC 3klfC 3klgC 3kliC 1n5yS 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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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 64988.590 Da / Num. of mol.: 1 / Mutation: M41L, D67N, K70R, T215Y, K219Q, C280S, Q258C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: BH10 / Gene: gag-pol / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H |
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#2: Protein | Mass: 51120.605 Da / Num. of mol.: 1 / Mutation: C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: BH10 / Gene: gag-pol / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03366 |
-DNA chain , 2 types, 2 molecules EF
#5: DNA chain | Mass: 8367.386 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA TEMPLATE FOR REVERSE TRANSCRIPTASE |
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#6: DNA chain | Mass: 6490.267 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA PRIMER FOR REVERSE TRANSCRIPTASE |
-Antibody , 2 types, 2 molecules CD
#3: Antibody | Mass: 23362.650 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Strain: BALB/C / Cell: HYBRIDOMA |
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#4: Antibody | Mass: 24000.814 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Strain: BALB/C / Cell: HYBRIDOMA |
-Non-polymers , 2 types, 139 molecules
#7: Chemical | ChemComp-MG / |
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#8: Water | ChemComp-HOH / |
-Details
Sequence details | ACOORDING TO THE AUTHORS THERE IS POLYMORPHI |
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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: 4.95 Å3/Da / Density % sol: 75.17 % |
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Crystal grow | pH: 6 Details: 100 MM CACODYLATE PH 6.0, 31-34% SATURATED AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277.0K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 |
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Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 27, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.9→40 Å / Num. obs: 72879 / % possible obs: 94.2 % / Biso Wilson estimate: 41.6 Å2 / Rmerge(I) obs: 0.127 |
Reflection shell | Resolution: 2.9→3 Å / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 1.5 / % possible all: 87.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1N5Y Resolution: 2.9→24.79 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 7028202 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 26.01 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 74.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→24.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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