[English] 日本語
![](img/lk-miru.gif)
- PDB-1na8: Crystal structure of ADP-ribosylation factor binding protein GGA1 -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1na8 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of ADP-ribosylation factor binding protein GGA1 | ||||||
![]() | ADP-ribosylation factor binding protein GGA1 | ||||||
![]() | SIGNALING PROTEIN / MEMBRANE PROTEIN / clathrin-adaptor / GGA / appendage / beta-sandwich | ||||||
Function / homology | ![]() protein localization to ciliary membrane / Golgi to plasma membrane transport / Golgi to plasma membrane protein transport / retrograde transport, endosome to Golgi / protein localization to cell surface / TBC/RABGAPs / phosphatidylinositol binding / ubiquitin binding / intracellular protein transport / protein catabolic process ...protein localization to ciliary membrane / Golgi to plasma membrane transport / Golgi to plasma membrane protein transport / retrograde transport, endosome to Golgi / protein localization to cell surface / TBC/RABGAPs / phosphatidylinositol binding / ubiquitin binding / intracellular protein transport / protein catabolic process / trans-Golgi network / protein localization / small GTPase binding / positive regulation of protein catabolic process / early endosome membrane / early endosome / endosome membrane / Amyloid fiber formation / intracellular membrane-bounded organelle / Golgi apparatus / protein-containing complex / nucleoplasm / membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Lui, W.W. / Collins, B.M. / Hirst, J. / Motley, A. / Millar, C. / Schu, P. / Owen, D.J. / Robinson, M.S. | ||||||
![]() | ![]() Title: Binding partners for the COOH-terminal appendage domains of the GGAs and gamma-adaptin Authors: Lui, W.W. / Collins, B.M. / Hirst, J. / Motley, A. / Millar, C. / Schu, P. / Owen, D.J. / Robinson, M.S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 73 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 55.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 444.8 KB | Display | |
Data in XML | ![]() | 15.7 KB | Display | |
Data in CIF | ![]() | 21.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1gyuS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
| ||||||||||
Details | The assymetric unit contains a dimer of two identical chains but this dimer is not observed in solution |
-
Components
#1: Protein | Mass: 17353.209 Da / Num. of mol.: 2 / Fragment: appendage domain, Residues 494-639 of SWS Q9UJY5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 50.8 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: sodium citrate, ammonium sulphate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→57 Å / Num. obs: 16193 / % possible obs: 99 % / Observed criterion σ(F): 5.9 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 5.9 / % possible all: 99 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 57 Å / % possible obs: 99 % |
Reflection shell | *PLUS % possible obs: 99 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ID 1GYU Resolution: 2.3→15 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.906 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS refinement used / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.119 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→15 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.358 Å / Total num. of bins used: 20 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 15 Å / Rfactor Rfree: 0.279 / Rfactor Rwork: 0.219 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 2.36 Å |