+Open data
-Basic information
Entry | Database: PDB / ID: 8amz | |||||||||
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Title | Spinach 19S proteasome | |||||||||
Components |
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Keywords | PLANT PROTEIN / PROTEASOME / UPS / PLANT / SPINACH | |||||||||
Function / homology | Function and homology information nuclear proteasome complex / : / metal-dependent deubiquitinase activity / proteasome regulatory particle / cytosolic proteasome complex / proteasome regulatory particle, lid subcomplex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / K63-linked deubiquitinase activity / proteasome binding ...nuclear proteasome complex / : / metal-dependent deubiquitinase activity / proteasome regulatory particle / cytosolic proteasome complex / proteasome regulatory particle, lid subcomplex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / K63-linked deubiquitinase activity / proteasome binding / regulation of protein catabolic process / protein deubiquitination / proteasome storage granule / polyubiquitin modification-dependent protein binding / positive regulation of RNA polymerase II transcription preinitiation complex assembly / enzyme regulator activity / : / proteasome complex / protein catabolic process / metallopeptidase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / membrane => GO:0016020 / structural molecule activity / ATP hydrolysis activity / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Spinacia oleracea (spinach) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Kandolf, S. / Grishkovskaya, I. / Meinhart, A. / Haselbach, D. | |||||||||
Funding support | 1items
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Citation | Journal: Plant Communications / Year: 2022 Title: Cryo-EM structure of the plant 26S proteasome Authors: Kandolf, S. / Grishkovskaya, I. / Belacic, K. / Foster, B. / Imre, R. / Bolhuis, D.L. / Mechtler, K. / Schleiffer, A. / Tagare, H. / Zhong, E.D. / Meinhart, A. / Brown, N.G. / Haselbach, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8amz.cif.gz | 973.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8amz.ent.gz | 668 KB | Display | PDB format |
PDBx/mmJSON format | 8amz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/8amz ftp://data.pdbj.org/pub/pdb/validation_reports/am/8amz | HTTPS FTP |
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-Related structure data
Related structure data | M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
EM raw data | EMPIAR-10974 (Title: Cryo-EM structure of the plant 26S proteasome / Data size: 7.9 TB Data #1: Unaligned multi-frame micrographs of spinach 26S proteasome [micrographs - multiframe] Data #2: Unaligned multi-frame micrographs of spinach 26S proteasome [micrographs - multiframe] Data #3: Unaligned multi-frame micrographs of spinach 26S proteasome [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-26S proteasome regulatory subunit ... , 2 types, 2 molecules HV
#1: Protein | Mass: 47786.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q41365 |
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#7: Protein | Mass: 34506.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QHF5 |
-AAA domain-containing ... , 5 types, 5 molecules IJKLM
#2: Protein | Mass: 49635.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QMF8 |
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#3: Protein | Mass: 45810.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QG12 |
#4: Protein | Mass: 47132.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QSR5 |
#5: Protein | Mass: 44596.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RWB0 |
#6: Protein | Mass: 47754.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QR38 |
-PCI domain-containing ... , 6 types, 6 molecules STOQPR
#8: Protein | Mass: 55356.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R856 |
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#9: Protein | Mass: 30804.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RR58 |
#11: Protein | Mass: 44242.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RRW6 |
#13: Protein | Mass: 47236.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QD81 |
#14: Protein | Mass: 50790.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QUR6 |
#17: Protein | Mass: 44432.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QVX1 |
-Protein , 2 types, 2 molecules WU
#10: Protein | Mass: 42562.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QPY6 |
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#12: Protein | Mass: 34457.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RYG8 |
-26S proteasome non-ATPase regulatory subunit ... , 2 types, 2 molecules ZN
#15: Protein | Mass: 98484.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RA51 |
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#16: Protein | Mass: 109199.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RNX4 |
-Non-polymers , 2 types, 2 molecules
#18: Chemical | ChemComp-ATP / |
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#19: Chemical | ChemComp-ADP / |
-Details
Has ligand of interest | N |
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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: Spinach 26S proteasome / Type: COMPLEX / Entity ID: #1-#17 / Source: NATURAL | |||||||||||||||||||||||||||||||||||||||||||||
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Molecular weight | Value: 1.7 MDa / Experimental value: YES | |||||||||||||||||||||||||||||||||||||||||||||
Source (natural) | Organism: Spinacia oleracea (spinach) | |||||||||||||||||||||||||||||||||||||||||||||
Buffer solution | pH: 6.5 | |||||||||||||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.02 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R3.5/1 | |||||||||||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 277 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 FIELDBright-field microscopy / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: ZEMLIN TABLEAU | ||||||||||||||||||
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER | ||||||||||||||||||
Image recording |
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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: 951422 | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 951422 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 109.9 / Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6MSB |