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Yorodumi- PDB-5lzp: Binding of the C-terminal GQYL motif of the bacterial proteasome ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lzp | ||||||
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Title | Binding of the C-terminal GQYL motif of the bacterial proteasome activator Bpa to the 20S proteasome | ||||||
Components |
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Keywords | HYDROLASE / Proteasome / Proteasome activator / protein degradation / complex | ||||||
Function / homology | Function and homology information 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 / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / proteasomal protein catabolic process ...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 / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / proteasomal protein catabolic process / 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 Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Bolten, M. / Delley, C.L. / Leibundgut, M. / Boehringer, D. / Ban, N. / Weber-Ban, E. | ||||||
Citation | Journal: Structure / Year: 2016 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5lzp.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5lzp.ent.gz | 939.8 KB | Display | PDB format |
PDBx/mmJSON format | 5lzp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lzp_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5lzp_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5lzp_validation.xml.gz | 148.9 KB | Display | |
Data in CIF | 5lzp_validation.cif.gz | 235 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lz/5lzp ftp://data.pdbj.org/pub/pdb/validation_reports/lz/5lzp | HTTPS FTP |
-Related structure data
Related structure data | 4128MC 4127C 5lfjC 5lfpC 5lfqC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 26024.971 Da / Num. of mol.: 14 / Mutation: M1_I7del Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Gene: prcA, Rv2109c / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P9WHU1, proteasome endopeptidase complex #2: Protein | Mass: 19792.113 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Gene: bpa, Rv3780, MTCY13D12.14 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WKX3 #3: Protein | Mass: 25457.504 Da / Num. of mol.: 14 / Mutation: T1A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Gene: prcB, Rv2110c / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P9WHT9, proteasome endopeptidase complex |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: proteasome in complex with bacterial proteasome activator Type: COMPLEX / Entity ID: #1-#7 / Source: MULTIPLE SOURCES | |||||||||||||||
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Molecular weight | Value: 0.93 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Mycobacterium tuberculosis H37Rv (bacteria) / Cellular location: cytoplasm | |||||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) | |||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 0.102 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Details: Quantifoil R 2/2 with an additional thin carbon layer Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/2 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 280.5 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 100000 X / Nominal defocus max: 3600 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 25 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 Details: Drift corrected in post-processing. 4 images per hole. |
Image scans | Sampling size: 14 µm / Movie frames/image: 7 |
-Processing
Software | Name: PHENIX / Version: (1.10_2155: ???) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C7 (7 fold cyclic) | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48799 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | |||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 3.5→3.5 Å / SU ML: 0.73 / σ(F): 1.99 / Phase error: 34.64 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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