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- PDB-3ds4: HIV-1 capsid C-terminal domain mutant (L211S) in complex with an ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ds4 | ||||||
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Title | HIV-1 capsid C-terminal domain mutant (L211S) in complex with an inhibitor of particle assembly (CAI) | ||||||
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![]() | VIRAL PROTEIN / HIV / capsid / mutant / inhibitor / assembly / polyprotein / complex(viral protein-peptide) / mainly alpha | ||||||
Function / homology | ![]() viral budding via host ESCRT complex / 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 ...viral budding via host ESCRT complex / 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 / DNA recombination / host cell cytoplasm / 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 / RNA binding / zinc ion binding / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Igonet, S. / Vaney, M.C. / Rey, F.A. | ||||||
![]() | ![]() Title: Residues in the HIV-1 Capsid Assembly Inhibitor Binding Site Are Essential for Maintaining the Assembly-competent Quaternary Structure of the Capsid Protein. Authors: Bartonova, V. / Igonet, S. / Sticht, J. / Glass, B. / Habermann, A. / Vaney, M.C. / Sehr, P. / Lewis, J. / Rey, F.A. / Krausslich, H.G. #1: ![]() Title: The HIV-1 capsid protein C-terminal domain in complex with a virus assembly inhibitor Authors: Ternois, F. / Sticht, J. / Duquerroy, S. / Krausslich, H.-G. / Rey, F.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.1 KB | Display | ![]() |
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PDB format | ![]() | 67.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3dphC ![]() 3ds0C ![]() 3ds1C ![]() 3ds2C ![]() 3ds3C ![]() 3ds5C ![]() 3dtjC ![]() 2buoS 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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Unit cell |
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Components
#1: Protein | Mass: 9504.841 Da / Num. of mol.: 2 / Fragment: C-terminal domain, UNP residues 278-363 / Mutation: L211S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | | Mass: 1445.570 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: CAI peptide was obtained as lyophilized trifluoroacetic acid salts. #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.02 % |
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Crystal grow | Temperature: 298 K / Method: evaporation Details: PEG4000, 200mM ammonium sulfate, EVAPORATION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 17, 2007 |
Radiation | Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.008 Å / Relative weight: 1 |
Reflection | Resolution: 1.12→41.2 Å / Num. obs: 63254 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.12→1.19 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.41 / % possible all: 73.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2BUO Resolution: 1.12→35.4 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.5 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.054 Å2
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Refinement step | Cycle: LAST / Resolution: 1.12→35.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.12→1.149 Å / Total num. of bins used: 20
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