[English] 日本語
![](img/lk-miru.gif)
- PDB-7rar: Structure of Q67H mutant of disulfide stabilized HIV-1 CA hexamer -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7rar | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of Q67H mutant of disulfide stabilized HIV-1 CA hexamer | ||||||||||||
![]() | Capsid protein p24 | ||||||||||||
![]() | VIRAL PROTEIN | ||||||||||||
Function / homology | ![]() viral budding via host ESCRT complex / ISG15 antiviral mechanism / host multivesicular body / viral nucleocapsid / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Bester, S.M. / Kvaratskhelia, M. | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() Title: Structural and Mechanistic Bases of Viral Resistance to HIV-1 Capsid Inhibitor Lenacapavir. Authors: Bester, S.M. / Adu-Ampratwum, D. / Annamalai, A.S. / Wei, G. / Briganti, L. / Murphy, B.C. / Haney, R. / Fuchs, J.R. / Kvaratskhelia, M. | ||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 120.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 76.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 419.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 421.1 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 16.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7rhmC ![]() 7rhnC ![]() 7rj2C ![]() 7rj4C ![]() 7rmjC ![]() 7rmmC ![]() 3h47S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| x 6||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 25471.291 Da / Num. of mol.: 1 / Mutation: A14C, E45C, Q67H, W184A, M185A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-IOD / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.47 % |
---|---|
Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop Details: 0.425M NaI, 4% peg 3350, 6% glycerol, 0.1M sodium cacodylate trihydrate pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Oct 13, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→46.75 Å / Num. obs: 15259 / % possible obs: 100 % / Redundancy: 10.8 % / Biso Wilson estimate: 27.73 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.182 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.15→2.22 Å / Redundancy: 10.2 % / Rmerge(I) obs: 1.59 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1325 / CC1/2: 0.667 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3H47 Resolution: 2.15→46.75 Å / SU ML: 0.2285 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.6613 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→46.75 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: C / Label asym-ID: A
|