[English] 日本語
![](img/lk-miru.gif)
- PDB-8pfd: Crystal structure of binary complex between Aster yellows witches... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8pfd | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of binary complex between Aster yellows witches'-broom phytoplasma effector SAP05 and the von Willebrand Factor Type A domain of the proteasomal ubiquitin receptor Rpn10 from Arabidopsis thaliana | |||||||||||||||
![]() |
| |||||||||||||||
![]() | PROTEIN BINDING / Targeted protein degradation / ubiquitin-independent / bacterial effector protein / 26S proteasome | |||||||||||||||
Function / homology | ![]() stamen formation / post-embryonic root development / response to cytokinin / root hair elongation / regulation of seed germination / peptide receptor activity / response to misfolded protein / leaf senescence / leaf development / pollen development ...stamen formation / post-embryonic root development / response to cytokinin / root hair elongation / regulation of seed germination / peptide receptor activity / response to misfolded protein / leaf senescence / leaf development / pollen development / response to auxin / response to sucrose / response to abscisic acid / proteasome regulatory particle, base subcomplex / proteasome assembly / polyubiquitin modification-dependent protein binding / response to salt stress / proteasome complex / protein catabolic process / response to heat / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA damage response / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Huang, W. / Liu, Q. / Maqbool, A. / Stevenson, C.E.M. / Lawson, D.M. / Kamoun, S. / Hogenhout, S.A. | |||||||||||||||
Funding support | ![]() ![]()
| |||||||||||||||
![]() | ![]() Title: Bimodular architecture of bacterial effector SAP05 that drives ubiquitin-independent targeted protein degradation. Authors: Liu, Q. / Maqbool, A. / Mirkin, F.G. / Singh, Y. / Stevenson, C.E.M. / Lawson, D.M. / Kamoun, S. / Huang, W. / Hogenhout, S.A. #1: ![]() Title: Bimodular architecture of bacterial effector SAP05 drives ubiquitin-independent targeted protein degradation Authors: Liu, Q. / Maqbool, A. / Mirkin, F.G. / Singh, Y. / Stevenson, C.E.M. / Lawson, D.M. / Kamoun, S. / Huang, W. / Hogenhout, S.A. | |||||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 126.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 97.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 433.5 KB | Display | |
Data in XML | ![]() | 12 KB | Display | |
Data in CIF | ![]() | 15.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8pfcC C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 12310.920 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The crystallized sequence corresponds to residues 33-135 of the full 135-residue wild-type sequence, which is prepended by a GLY-PRO dipeptide left over from cleavage of the affinity tag. Source: (gene. exp.) ![]() Gene: AYWB_032 / Production host: ![]() ![]() |
---|---|
#2: Protein | Mass: 20879.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The crystallized sequence corresponds to residues 2-193 of the full 386-residue wild-type sequence. The native N-terminal MET is replaced by a GLY-PRO dipeptide left over from cleavage of the affinity tag. Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.7 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: NULL |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 25, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→68.6 Å / Num. obs: 15199 / % possible obs: 100 % / Redundancy: 13.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.033 / Rrim(I) all: 0.122 / Χ2: 0.94 / Net I/σ(I): 10.9 / Num. measured all: 210355 |
Reflection shell | Resolution: 2.17→2.24 Å / % possible obs: 99.9 % / Redundancy: 13.6 % / Rmerge(I) obs: 2.599 / Num. measured all: 18117 / Num. unique obs: 1337 / CC1/2: 0.436 / Rpim(I) all: 0.729 / Rrim(I) all: 2.7 / Χ2: 0.93 / Net I/σ(I) obs: 1 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 59.824 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.17→49.84 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|