+Open data
-Basic information
Entry | Database: PDB / ID: 3h47 | ||||||
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Title | X-ray Structure of Hexameric HIV-1 CA | ||||||
Components | Capsid protein p24 | ||||||
Keywords | VIRAL PROTEIN / capsid protein / hexamer / engineered disulfide bonds | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Pornillos, O. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2009 Title: X-ray structures of the hexameric building block of the HIV capsid. Authors: Pornillos, O. / Ganser-Pornillos, B.K. / Kelly, B.N. / Hua, Y. / Whitby, F.G. / Stout, C.D. / Sundquist, W.I. / Hill, C.P. / Yeager, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3h47.cif.gz | 57.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h47.ent.gz | 40.1 KB | Display | PDB format |
PDBx/mmJSON format | 3h47.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h4/3h47 ftp://data.pdbj.org/pub/pdb/validation_reports/h4/3h47 | HTTPS FTP |
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-Related structure data
Related structure data | 3gv2C 3h4eC 2buoS 2pxrS 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
#1: Protein | Mass: 25461.271 Da / Num. of mol.: 1 / Fragment: UNP residues 133-363 / Mutation: A14C,E45C,W184A,M185A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) Strain: NL4-3 / Gene: CA, gag-pol / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12497 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.91 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 10-12% PEG 8,000, 100 mM sodium malonate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
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Detector | Date: Jul 18, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 21352 / % possible obs: 99.9 % / Redundancy: 10.5 % / Biso Wilson estimate: 23.5 Å2 / Rsym value: 0.1 / Net I/σ(I): 21.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 2PXR - with residues 1-14 and 87-100 deleted, PDB 2BUO - with residues 175-190 deleted Resolution: 1.9→26.74 Å / SU ML: 0.32 / σ(F): 1.34 / 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 / Bsol: 41.415 Å2 / ksol: 0.329 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→26.74 Å
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LS refinement shell |
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