[English] 日本語
![](img/lk-miru.gif)
- EMDB-4128: Binding of the C-terminal GQYL motif of the bacterial proteasome ... -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-4128 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Binding of the C-terminal GQYL motif of the bacterial proteasome activator Bpa to the 20S proteasome | |||||||||
![]() | ||||||||||
![]() |
| |||||||||
![]() | Proteasome / Proteasome activator / protein degradation / complex / hydrolase | |||||||||
Function / homology | ![]() symbiont-mediated perturbation of host defenses / proteasome accessory complex / positive regulation of proteasomal protein catabolic process / zymogen binding / proteasome binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasomal protein catabolic process / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity ...symbiont-mediated perturbation of host defenses / proteasome accessory complex / positive regulation of proteasomal protein catabolic process / zymogen binding / proteasome binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasomal protein catabolic process / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / peptidoglycan-based cell wall / proteolysis involved in protein catabolic process / protein homooligomerization / modification-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / extracellular region / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
![]() | Bolten M / Delley CL | |||||||||
![]() | ![]() Title: Structural Analysis of the Bacterial Proteasome Activator Bpa in Complex with the 20S Proteasome. Authors: Marcel Bolten / Cyrille L Delley / Marc Leibundgut / Daniel Boehringer / Nenad Ban / Eilika Weber-Ban / ![]() Abstract: Mycobacterium tuberculosis harbors proteasomes that recruit substrates for degradation through an ubiquitin-like modification pathway. Recently, a non-ATPase activator termed Bpa (bacterial ...Mycobacterium tuberculosis harbors proteasomes that recruit substrates for degradation through an ubiquitin-like modification pathway. Recently, a non-ATPase activator termed Bpa (bacterial proteasome activator) was shown to support an alternate proteasomal degradation pathway. Here, we present the cryo-electron microscopy (cryo-EM) structure of Bpa in complex with the 20S core particle (CP). For docking into the cryo-EM density, we solved the X-ray structure of Bpa, showing that it forms tight four-helix bundles arranged into a 12-membered ring with a 40 Å wide central pore and the C-terminal helix of each protomer protruding from the ring. The Bpa model was fitted into the cryo-EM map of the Bpa-CP complex, revealing its architecture and striking symmetry mismatch. The Bpa-CP interface was resolved to 3.5 Å, showing the interactions between the C-terminal GQYL motif of Bpa and the proteasome α-rings. This docking mode is related to the one observed for eukaryotic activators with features specific to the bacterial complex. | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 201.3 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 15.5 KB 15.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.3 KB | Display | ![]() |
Images | ![]() | 163.7 KB | ||
Filedesc metadata | ![]() | 6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 268.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 268 KB | Display | |
Data in XML | ![]() | 13.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5lzpMC ![]() 4127C ![]() 5lfjC ![]() 5lfpC ![]() 5lfqC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
-Entire : proteasome in complex with bacterial proteasome activator
Entire | Name: proteasome in complex with bacterial proteasome activator |
---|---|
Components |
|
-Supramolecule #1: proteasome in complex with bacterial proteasome activator
Supramolecule | Name: proteasome in complex with bacterial proteasome activator type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7 |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 930 KDa |
-Macromolecule #1: Proteasome subunit alpha
Macromolecule | Name: Proteasome subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 26.024971 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: SPEQAMRERS ELARKGIARA KSVVALAYAG GVLFVAENPS RSLQKISELY DRVGFAAAGK FNEFDNLRRG GIQFADTRGY AYDRRDVTG RQLANVYAQT LGTIFTEQAK PYEVELCVAE VAHYGETKRP ELYRITYDGS IADEPHFVVM GGTTEPIANA L KESYAENA ...String: SPEQAMRERS ELARKGIARA KSVVALAYAG GVLFVAENPS RSLQKISELY DRVGFAAAGK FNEFDNLRRG GIQFADTRGY AYDRRDVTG RQLANVYAQT LGTIFTEQAK PYEVELCVAE VAHYGETKRP ELYRITYDGS IADEPHFVVM GGTTEPIANA L KESYAENA SLTDALRIAV AALRAGSADT SGGDQPTLGV ASLEVAVLDA NRPRRAFRRI TGSALQALLV DQESPQSDGE SS G UniProtKB: Proteasome subunit alpha |
-Macromolecule #2: Bacterial proteasome activator
Macromolecule | Name: Bacterial proteasome activator / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 19.792113 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MHHHHHHVIG LSTGSDDDDV EVIGGVDPRL IAVQENDSDE SSLTDLVEQP AKVMRIGTMI KQLLEEVRAA PLDEASRNRL RDIHATSIR ELEDGLAPEL REELDRLTLP FNEDAVPSDA ELRIAQAQLV GWLEGLFHGI QTALFAQQMA ARAQLQQMRQ G ALPPGVGK SGQHGHGTGQ YL UniProtKB: Bacterial proteasome activator |
-Macromolecule #3: Proteasome subunit beta
Macromolecule | Name: Proteasome subunit beta / type: protein_or_peptide / ID: 3 / Number of copies: 14 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 25.457504 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: ATIVALKYPG GVVMAGDRRS TQGNMISGRD VRKVYITDDY TATGIAGTAA VAVEFARLYA VELEHYEKLE GVPLTFAGKI NRLAIMVRG NLAAAMQGLL ALPLLAGYDI HASDPQSAGR IVSFDAAGGW NIEEEGYQAV GSGSLFAKSS MKKLYSQVTD G DSGLRVAV ...String: ATIVALKYPG GVVMAGDRRS TQGNMISGRD VRKVYITDDY TATGIAGTAA VAVEFARLYA VELEHYEKLE GVPLTFAGKI NRLAIMVRG NLAAAMQGLL ALPLLAGYDI HASDPQSAGR IVSFDAAGGW NIEEEGYQAV GSGSLFAKSS MKKLYSQVTD G DSGLRVAV EALYDAADDD SATGGPDLVR GIFPTAVIID ADGAVDVPES RIAELARAII ESRSGADTFG SDGGEKWSHP QF EK UniProtKB: Proteasome subunit beta |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 0.102 mg/mL | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.5 Component:
| |||||||||
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 22 sec. / Pretreatment - Atmosphere: OTHER Details: Quantifoil R 2/2 with an additional thin carbon layer | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 280.5 K / Instrument: FEI VITROBOT MARK I |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Average electron dose: 25.0 e/Å2 Details: Drift corrected in post-processing. 4 images per hole. |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 100000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.6 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
+
Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
---|---|
Output model | ![]() PDB-5lzp: |