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Open data
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Basic information
Entry | Database: PDB / ID: 8u6y | ||||||
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Title | Preholo-Proteasome from Beta 3 D205 deletion | ||||||
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Function / homology | ![]() regulation of proteasome core complex assembly / proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / proteasome storage granule / endopeptidase activator activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Walsh Jr., R.M. / Rawson, S. / Velez, B. / Blickling, M. / Razi, A. / Hanna, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanism of autocatalytic activation during proteasome assembly. Authors: Benjamin Velez / Richard M Walsh / Shaun Rawson / Aida Razi / Lea Adams / Erignacio Fermin Perez / Fenglong Jiao / Marie Blickling / Tamayanthi Rajakumar / Darlene Fung / Lan Huang / John Hanna / ![]() Abstract: Many large molecular machines are too elaborate to assemble spontaneously and are built through ordered pathways orchestrated by dedicated chaperones. During assembly of the core particle (CP) of the ...Many large molecular machines are too elaborate to assemble spontaneously and are built through ordered pathways orchestrated by dedicated chaperones. During assembly of the core particle (CP) of the proteasome, where protein degradation occurs, its six active sites are simultaneously activated via cleavage of N-terminal propeptides. Such activation is autocatalytic and coupled to fusion of two half-CP intermediates, which protects cells by preventing activation until enclosure of the active sites within the CP interior. Here we uncover key mechanistic aspects of autocatalytic activation, which proceeds through alignment of the β5 and β2 catalytic triad residues, respectively, with these triads being misaligned before fusion. This mechanism contrasts with most other zymogens, in which catalytic centers are preformed. Our data also clarify the mechanism by which individual subunits can be added in a precise, temporally ordered manner. This work informs two decades-old mysteries in the proteasome field, with broader implications for protease biology and multisubunit complex assembly. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2.6 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 41963MC ![]() 8u7uC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Proteasome subunit alpha type- ... , 7 types, 14 molecules ARBSCTDUEVFWGX
#1: Protein | ![]() Mass: 28033.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() References: UniProt: P21243, ![]() #2: Protein | ![]() Mass: 27191.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() References: UniProt: P23639, ![]() #3: Protein | ![]() Mass: 27181.609 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #4: Protein | ![]() Mass: 28478.111 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() References: UniProt: P40303, ![]() #5: Protein | ![]() Mass: 28649.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() References: UniProt: P32379, ![]() #6: Protein | ![]() Mass: 25634.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() References: UniProt: P40302, ![]() #7: Protein | ![]() Mass: 31575.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() References: UniProt: P21242, ![]() |
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-Protein , 3 types, 6 molecules HYOfPg
#8: Protein | Mass: 16777.766 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #15: Protein | Mass: 30718.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #16: Protein | Mass: 30762.895 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
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-Proteasome subunit beta type- ... , 7 types, 14 molecules IZJaKbLcMdNeQh
#9: Protein | ![]() Mass: 28299.889 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() References: UniProt: P25043, ![]() #10: Protein | ![]() Mass: 22512.754 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #11: Protein | ![]() Mass: 22545.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() References: UniProt: P22141, ![]() #12: Protein | ![]() Mass: 31670.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() References: UniProt: P30656, ![]() #13: Protein | ![]() Mass: 26905.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() References: UniProt: P23724, ![]() #14: Protein | ![]() Mass: 23573.604 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() References: UniProt: P38624, ![]() #17: Protein | ![]() Mass: 29471.289 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() References: UniProt: P30657, ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: Preholo-proteasome from Beta 3 D205 deletion mutant / Type: COMPLEX Details: D205 is terminal most residue in the Beta 3 subunit. The deletion of this residue causes an accumulation of assembly intermediates including the Preholo-Proteasome Entity ID: all / Source: NATURAL | ||||||||||||||||||||
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Molecular weight | Value: 0.75 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: ![]() ![]() ![]() | ||||||||||||||||||||
Buffer solution | pH: 7.5 Details: Fluorinated Fos-Choline was added immediately prior to deposition on a grid for plunge freezing. | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 4.48 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification![]() | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295.15 K |
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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![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() ![]() |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 3.995 sec. / Electron dose: 57 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7461 |
EM imaging optics | Energyfilter name![]() |
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Processing
EM software |
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1146597 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19020 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 8T08 Accession code: 8T08 / Source name: PDB / Type: experimental model |