[English] 日本語
![](img/lk-miru.gif)
- PDB-3ds1: HIV-1 capsid C-terminal domain mutant (E187A) in complex with an ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3ds1 | ||||||
---|---|---|---|---|---|---|---|
Title | HIV-1 capsid C-terminal domain mutant (E187A) in complex with an inhibitor of particle assembly (CAI) | ||||||
![]() |
| ||||||
![]() | 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 | ![]() ![]() ![]() | ||||||
![]() | Vaney, M.-C. / Igonet, S. / 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 52.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 37.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 3dphC ![]() 3ds0C ![]() 3ds2C ![]() 3ds3C ![]() 3ds4C ![]() 3ds5C ![]() 3dtjC ![]() 2buoS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
| ||||||||
Details | AUTHORS STATE THAT THE ASYMMETRIC UNIT IS COMPOSED OF A HETERODIMER OF CHAIN A IN COMPLEX WITH THE INHIBITOR OF PARTICLE ASSEMBLY (CHAIN T). TO BUILD THE BIOLOGICAL HOMODIMER, ONE SHOULD APPLY THE TRANSFORMATION MATRICES DEFINED BELOW ON THE TWO CHAINS A AND T. |
-
Components
#1: Protein | Mass: 9472.884 Da / Num. of mol.: 1 / Fragment: C-terminal domain, UNP residues 278-363 / Mutation: E187A 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 / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.7 % |
---|---|
Crystal grow | Temperature: 298 K / Method: evaporation / pH: 4.2 Details: 30% PEG 4000, 100mM ammonium acetate, 10mM MgCl2, pH 4.2, EVAPORATION, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 25, 2007 / Details: Dynamically bendable mirror |
Radiation | Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.044 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→38.8 Å / Num. obs: 11802 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 73.8 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 19.7 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 9.7 / Rsym value: 0.368 / % possible all: 98.6 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 2BUO Resolution: 1.6→31.17 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.628 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 24.749 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→31.17 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.601→1.643 Å / Total num. of bins used: 20
|