[English] 日本語
![](img/lk-miru.gif)
- PDB-4jpo: 5A resolution structure of Proteasome Assembly Chaperone Hsm3 in ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4jpo | ||||||
---|---|---|---|---|---|---|---|
Title | 5A resolution structure of Proteasome Assembly Chaperone Hsm3 in complex with a C-terminal fragment of Rpt1 | ||||||
![]() |
| ||||||
![]() | CHAPERONE/HYDROLASE / Hsm3 / Chaperone / Proteasome / Protein Complex / CHAPERONE-HYDROLASE complex | ||||||
Function / homology | ![]() proteasome regulatory particle assembly / proteasome-activating activity / proteasome regulatory particle, base subcomplex / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation ...proteasome regulatory particle assembly / proteasome-activating activity / proteasome regulatory particle, base subcomplex / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of RNA polymerase II transcription preinitiation complex assembly / Ub-specific processing proteases / mismatch repair / protein folding chaperone / Neutrophil degranulation / proteasome complex / positive regulation of protein catabolic process / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitin protein ligase binding / ATP hydrolysis activity / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Lovell, S. / Battaile, K.P. / Singh, R. / Roelofs, J. | ||||||
![]() | ![]() Title: Reconfiguration of the proteasome during chaperone-mediated assembly. Authors: Soyeon Park / Xueming Li / Ho Min Kim / Chingakham Ranjit Singh / Geng Tian / Martin A Hoyt / Scott Lovell / Kevin P Battaile / Michal Zolkiewski / Philip Coffino / Jeroen Roelofs / Yifan ...Authors: Soyeon Park / Xueming Li / Ho Min Kim / Chingakham Ranjit Singh / Geng Tian / Martin A Hoyt / Scott Lovell / Kevin P Battaile / Michal Zolkiewski / Philip Coffino / Jeroen Roelofs / Yifan Cheng / Daniel Finley / ![]() Abstract: The proteasomal ATPase ring, comprising Rpt1-Rpt6, associates with the heptameric α-ring of the proteasome core particle (CP) in the mature proteasome, with the Rpt carboxy-terminal tails inserting ...The proteasomal ATPase ring, comprising Rpt1-Rpt6, associates with the heptameric α-ring of the proteasome core particle (CP) in the mature proteasome, with the Rpt carboxy-terminal tails inserting into pockets of the α-ring. Rpt ring assembly is mediated by four chaperones, each binding a distinct Rpt subunit. Here we report that the base subassembly of the Saccharomyces cerevisiae proteasome, which includes the Rpt ring, forms a high-affinity complex with the CP. This complex is subject to active dissociation by the chaperones Hsm3, Nas6 and Rpn14. Chaperone-mediated dissociation was abrogated by a non-hydrolysable ATP analogue, indicating that chaperone action is coupled to nucleotide hydrolysis by the Rpt ring. Unexpectedly, synthetic Rpt tail peptides bound α-pockets with poor specificity, except for Rpt6, which uniquely bound the α2/α3-pocket. Although the Rpt6 tail is not visualized within an α-pocket in mature proteasomes, it inserts into the α2/α3-pocket in the base-CP complex and is important for complex formation. Thus, the Rpt-CP interface is reconfigured when the lid complex joins the nascent proteasome to form the mature holoenzyme. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 191.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 147.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 5593C ![]() 5611C ![]() 5612C ![]() 5613C ![]() 5614C ![]() 5615C ![]() 5616C ![]() 5617C ![]() 4fp7S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
5 | ![]()
| ||||||||
6 | ![]()
| ||||||||
7 |
| ||||||||
8 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 56685.719 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: HSM3, YBR272C, YBR1740 / Plasmid: pJR89 / Production host: ![]() ![]() #2: Protein | Mass: 11637.442 Da / Num. of mol.: 2 / Fragment: C-terminal fragment, UNP residues 379-467 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: RPT1, CIM5, YTA3, YKL145W / Plasmid: pJR89 / Production host: ![]() ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 Details: 3M Sodium Formate, 100 mM Bis-Tris, 10mM Calcium Chloride, pH 7.0, vapor diffusion, temperature 293K |
---|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 5→160.474 Å / Num. all: 16422 / Num. obs: 16422 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 19.3 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 5→5.59 Å / Redundancy: 19.2 % / Rmerge(I) obs: 0.971 / Mean I/σ(I) obs: 3.6 / Num. unique all: 4550 / % possible all: 100 |
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4FP7 Resolution: 5→46.87 Å / Cor.coef. Fo:Fc: 0.9254 / Cor.coef. Fo:Fc free: 0.9109 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: B-factors were set to the value determined from the Wilson plot for refinement.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 273 Å2 / Biso mean: 273 Å2 / Biso min: 273 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 2.055 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 5→46.87 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 5→5.34 Å / Total num. of bins used: 8
|