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Yorodumi- PDB-3phv: X-RAY ANALYSIS OF HIV-1 PROTEINASE AT 2.7 ANGSTROMS RESOLUTION CO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3phv | ||||||
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Title | X-RAY ANALYSIS OF HIV-1 PROTEINASE AT 2.7 ANGSTROMS RESOLUTION CONFIRMS STRUCTURAL HOMOLOGY AMONG RETROVIRAL ENZYMES | ||||||
Components | UNLIGANDED HIV-1 PROTEASE | ||||||
Keywords | HYDROLASE / ASPARTIC PROTEINASE | ||||||
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 | HIV-1 M:B_HXB2R (virus) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.7 Å | ||||||
Authors | Lapatto, R. / Blundell, T.L. / Hemmings, A. / Wilderspin, A. / Wood, S.P. / Danley, D.E. / Geoghegan, K.F. / Hawrylik, S.J. / Hobart, P.M. | ||||||
Citation | Journal: Nature / Year: 1989 Title: X-ray analysis of HIV-1 proteinase at 2.7 A resolution confirms structural homology among retroviral enzymes. Authors: Lapatto, R. / Blundell, T. / Hemmings, A. / Overington, J. / Wilderspin, A. / Wood, S. / Merson, J.R. / Whittle, P.J. / Danley, D.E. / Geoghegan, K.F. / Hawrylik, S.J. / Lee, S.E. / Scheld, K.G. / Hobart, P.M. #1: Journal: J.Biol.Chem. / Year: 1989 Title: Crystallization of the Aspartyl Protease from the Human Immunodeficiency Virus, HIV-1 Authors: Mckeever, B.M. / Navia, M.A. / Fitzgerald, P.M.D. / Springer, J.P. / Leu, C.-T. / Heimbach, J.C. / Herber, W.K. / Sigal, I.S. / Darke, P.L. | ||||||
History |
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Remark 700 | SHEET THE DIMER INTERFACE IS COMPOSED OF INTERDIGITATED N- AND C-TERMINAL STRANDS FROM BOTH ...SHEET THE DIMER INTERFACE IS COMPOSED OF INTERDIGITATED N- AND C-TERMINAL STRANDS FROM BOTH SUBUNITS FORMING A FOUR-STRANDED ANTI-PARALLEL BETA-SHEET, S2. APPLICATION OF THE TWO-FOLD ROTATION TO RESIDUES 1 TO 5 AND 95 TO 99 GENERATES RESIDUES 1' TO 5' AND 95' TO 99' RESPECTIVELY. BECAUSE OF LIMITATIONS IMPOSED BY THE PROTEIN DATA BANK FORMAT IT IS NOT POSSIBLE TO PRESENT THIS SHEET ON SHEET RECORDS. INSTEAD THIS SHEET IS SPECIFIED IN THIS REMARK. STRANDS 1 AND 3 ARE FROM THE MOLECULE IN THIS ENTRY AND STRANDS 2 AND 4 ARE FROM THE SYMMETRY RELATED MOLECULE. 1 S2 4 PRO 1 LEU 5 0 2 S2 4 CYS 95' PHE 99'-1 3 S2 4 CYS 95 PHE 99 -1 4 S2 4 PRO 1' LEU 5'-1 |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3phv.cif.gz | 28.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3phv.ent.gz | 18.3 KB | Display | PDB format |
PDBx/mmJSON format | 3phv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3phv_validation.pdf.gz | 365.3 KB | Display | wwPDB validaton report |
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Full document | 3phv_full_validation.pdf.gz | 375.6 KB | Display | |
Data in XML | 3phv_validation.xml.gz | 5 KB | Display | |
Data in CIF | 3phv_validation.cif.gz | 6.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/3phv ftp://data.pdbj.org/pub/pdb/validation_reports/ph/3phv | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10803.756 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HIV-1 M:B_HXB2R (virus) / Genus: Lentivirus / Species: Human immunodeficiency virus 1 / Cell line: S2 / Gene: POL / Organ: LEAVES / Gene (production host): POL / Production host: Escherichia coli (E. coli) / References: UniProt: P04585 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.66 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.7 Å / Num. obs: 2200 / Observed criterion σ(I): 2 / Num. measured all: 10000 / Rmerge(I) obs: 0.11 |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||
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Refinement | Resolution: 2.7→10 Å / σ(I): 3 /
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Refinement step | Cycle: LAST / Resolution: 2.7→10 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 10 Å / Num. reflection obs: 2370 / σ(I): 3 / Rfactor obs: 0.191 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |