+Open data
-Basic information
Entry | Database: PDB / ID: 1aum | ||||||
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Title | HIV CAPSID C-TERMINAL DOMAIN (CAC146) | ||||||
Components | HIV CAPSID | ||||||
Keywords | VIRAL PROTEIN / CORE PROTEIN / HIV / CAPSID / C-TERMINAL DOMAIN / CAC146 | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / 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 ...HIV-1 retropepsin / 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 / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / 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: 3 Å | ||||||
Authors | Hill, C.P. / Gamble, T.R. / Yoo, S. / Vajdos, F.F. / Von Schwedler, U.K. / Worthylake, D.K. / Wang, H. / Mccutcheon, J.P. / Sundquist, W.I. | ||||||
Citation | Journal: Science / Year: 1997 Title: Structure of the carboxyl-terminal dimerization domain of the HIV-1 capsid protein. Authors: Gamble, T.R. / Yoo, S. / Vajdos, F.F. / von Schwedler, U.K. / Worthylake, D.K. / Wang, H. / McCutcheon, J.P. / Sundquist, W.I. / Hill, C.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1aum.cif.gz | 27.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1aum.ent.gz | 18.4 KB | Display | PDB format |
PDBx/mmJSON format | 1aum.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1aum_validation.pdf.gz | 406.5 KB | Display | wwPDB validaton report |
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Full document | 1aum_full_validation.pdf.gz | 410.7 KB | Display | |
Data in XML | 1aum_validation.xml.gz | 5.3 KB | Display | |
Data in CIF | 1aum_validation.cif.gz | 6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/1aum ftp://data.pdbj.org/pub/pdb/validation_reports/au/1aum | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 7970.099 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, RESIDUES 146 - 231 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Cell line: BL21 / Plasmid: WISP97-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P12497 |
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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: 3.42 Å3/Da / Density % sol: 64.06 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 8 Details: CRYSTALS OF CAC(146-231) WERE GROWN AT 4C IN 8 MICROLITER SITTING DROPS CONTAINING A 1:1 MIXTURE OF PROTEIN SOLUTION (2.1 MM CA(151-231) IN 10 MM TRIS (PH 8.0) AND 2 MM 2-MERCAPTOETHANOL) ...Details: CRYSTALS OF CAC(146-231) WERE GROWN AT 4C IN 8 MICROLITER SITTING DROPS CONTAINING A 1:1 MIXTURE OF PROTEIN SOLUTION (2.1 MM CA(151-231) IN 10 MM TRIS (PH 8.0) AND 2 MM 2-MERCAPTOETHANOL) AND RESERVOIR SOLUTION (2.0 M AMMONIUM SULFATE), vapor diffusion - sitting drop | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
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: NSLS / Beamline: X12B |
Detector | Detector: CCD / Date: Jul 1, 1997 / Details: COLLIMATOR |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. obs: 2681 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Rsym value: 0.044 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.8→2.85 Å / Mean I/σ(I) obs: 2.5 / Rsym value: 0.368 / % possible all: 100 |
Reflection | *PLUS Rmerge(I) obs: 0.044 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.368 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: C-TERMINAL CAPSID (151 - 231) Resolution: 3→8 Å / σ(F): 0
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Displacement parameters | Biso mean: 43.44 Å2 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→8 Å
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||
Displacement parameters | *PLUS |