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Yorodumi- PDB-1hvu: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 REVERSE TRANSCRIPTASE COMPLEX... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hvu | ||||||
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Title | HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 REVERSE TRANSCRIPTASE COMPLEXED WITH A 33-BASE NUCLEOTIDE RNA PSEUDOKNOT | ||||||
Components |
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Keywords | TRANSFERASE/RNA / COMPLEX (NUCLEOTIDYLTRANSFERASE-RNA) / HYDROLASE / ASPARTYL PROTEASE / ENDONUCLEASE / TRANSFERASE-RNA 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 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.75 Å | ||||||
Authors | Jaeger, J. / Restle, T. / Steitz, T.A. | ||||||
Citation | Journal: EMBO J. / Year: 1998 Title: The structure of HIV-1 reverse transcriptase complexed with an RNA pseudoknot inhibitor. Authors: Jaeger, J. / Restle, T. / Steitz, T.A. #1: Journal: Structure / Year: 1994 Title: Comparison of Three Different Crystal Forms Shows HIV-1 Reverse Transcriptase Displays an Internal Swivel Motion Authors: Jaeger, J. / Smerdon, S.J. / Wang, J. / Boisvert, D.C. / Steitz, T.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hvu.cif.gz | 567.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hvu.ent.gz | 383.4 KB | Display | PDB format |
PDBx/mmJSON format | 1hvu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hvu_validation.pdf.gz | 414.4 KB | Display | wwPDB validaton report |
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Full document | 1hvu_full_validation.pdf.gz | 469.9 KB | Display | |
Data in XML | 1hvu_validation.xml.gz | 66.1 KB | Display | |
Data in CIF | 1hvu_validation.cif.gz | 109.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hv/1hvu ftp://data.pdbj.org/pub/pdb/validation_reports/hv/1hvu | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THE HIV-1 REVERSE TRANSCRIPTASE IS A HETERODIMER CONSISTING OF TWO SUBUNITS: P66 (CHAIN A) AND P51 (DESIGNATED CHAIN B) IN THIS CRYSTAL FORM THERE ARE FOUR REVERSE TRANSCRIPTASE MOLECULES PLUS FOUR RNA MOLECULES PER ASYMMETRIC UNIT. THE COORDINATES FOR ONE COMPLEX ARE CONTAINED IN THIS ENTRY. THE NON-CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS GIVEN BELOW ARE BASED ON THE BEST SUPERPOSITION OF THIS MOLECULE ON THE OTHER THREE HETERODIMER COMPLEXES. THE TRANSFORMATIONS MATRICES IN THE MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC SYMMETRY AMONG THE FOUR HETERODIMERS OF REVERSE TRANSCRIPTASE FOUND IN THE ASYMMETRIC UNIT. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD COORDINATES FOR THE OTHER THREE MOLECULES PRESENT IN THE ASYMMETRIC UNIT. |
-Components
#1: RNA chain | Mass: 9638.777 Da / Num. of mol.: 4 / Source method: obtained synthetically #2: Protein | Mass: 63834.125 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: THE HIV-1 REVERSE TRANSCRIPTASE IS A HETERODIMER CONSISTING OF TWO SUBUNITS: P66 (CHAIN A) AND P51 (DESIGNATED CHAIN B) IN THIS CRYSTAL FORM THERE ARE FOUR REVERSE TRANSCRIPTASE MOLECULES ...Details: THE HIV-1 REVERSE TRANSCRIPTASE IS A HETERODIMER CONSISTING OF TWO SUBUNITS: P66 (CHAIN A) AND P51 (DESIGNATED CHAIN B) IN THIS CRYSTAL FORM THERE ARE FOUR REVERSE TRANSCRIPTASE MOLECULES PLUS FOUR RNA MOLECULES PER ASYMMETRIC UNIT. THE COORDINATES FOR ONE COMPLEX ARE CONTAINED IN THIS ENTRY. THE NON-CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS GIVEN BELOW ARE BASED ON THE BEST SUPERPOSITION OF THIS MOLECULE ON THE OTHER THREE HETERODIMER COMPLEXES. Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Variant: BH10 ISOLATE / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase #3: Protein | Mass: 49532.961 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: THE HIV-1 REVERSE TRANSCRIPTASE IS A HETERODIMER CONSISTING OF TWO SUBUNITS: P66 (CHAIN A) AND P51 (DESIGNATED CHAIN B) IN THIS CRYSTAL FORM THERE ARE FOUR REVERSE TRANSCRIPTASE MOLECULES ...Details: THE HIV-1 REVERSE TRANSCRIPTASE IS A HETERODIMER CONSISTING OF TWO SUBUNITS: P66 (CHAIN A) AND P51 (DESIGNATED CHAIN B) IN THIS CRYSTAL FORM THERE ARE FOUR REVERSE TRANSCRIPTASE MOLECULES PLUS FOUR RNA MOLECULES PER ASYMMETRIC UNIT. THE COORDINATES FOR ONE COMPLEX ARE CONTAINED IN THIS ENTRY. THE NON-CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS GIVEN BELOW ARE BASED ON THE BEST SUPERPOSITION OF THIS MOLECULE ON THE OTHER THREE HETERODIMER COMPLEXES. Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Variant: BH10 ISOLATE / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase |
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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: 3.8 Å3/Da / Density % sol: 72 % | ||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.92 |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Mar 15, 1995 / Details: MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 4.75→30 Å / Num. obs: 32343 / % possible obs: 81 % / Observed criterion σ(I): 1.1 / Redundancy: 1.9 % / Rsym value: 0.064 |
Reflection | *PLUS Rmerge(I) obs: 0.064 |
Reflection shell | *PLUS % possible obs: 56.9 % / Rmerge(I) obs: 0.263 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HVT AND 1HMV Resolution: 4.75→30 Å / Cross valid method: FREE R / σ(F): 1.1 Details: RIGID BODY REFINEMENT ONLY DUE TO LIMITED RESOLUTION. THE FOLLOWING RESIDUES ARE NOT VISIBLE IN THE ELECTRON DENSITY MAPS, THEREFORE THEY ARE NOT INCLUDED IN THE COORDINATE LIST. CHAIN B: 212 - 234, 428 - 440.
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Displacement parameters | Biso mean: 55 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.75→30 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.853 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |