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Open data
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Basic information
Entry | Database: PDB / ID: 3h47 | ||||||
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Title | X-ray Structure of Hexameric HIV-1 CA | ||||||
![]() | Capsid protein p24 | ||||||
![]() | VIRAL PROTEIN / capsid protein / hexamer / engineered disulfide bonds | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pornillos, O. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 57.1 KB | Display | ![]() |
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PDB format | ![]() | 40.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 421.8 KB | Display | ![]() |
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Full document | ![]() | 425.2 KB | Display | |
Data in XML | ![]() | 11.4 KB | Display | |
Data in CIF | ![]() | 16.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3gv2C ![]() 3h4eC ![]() 2buoS ![]() 2pxrS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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.) ![]() Strain: NL4-3 / Gene: CA, gag-pol / Plasmid: pET11a / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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