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- PDB-7qve: Spinach 20S proteasome -

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Basic information

Entry
Database: PDB / ID: 7qve
TitleSpinach 20S proteasome
Components(Proteasome subunit ...) x 14
KeywordsPLANT PROTEIN / PROTEASOME / UPS / PLANT / SPINACH
Function / homology
Function and homology information


proteasome core complex / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / proteasomal protein catabolic process / peptidase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process ...proteasome core complex / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / proteasomal protein catabolic process / peptidase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / nucleus / cytosol / cytoplasm
Similarity search - Function
Proteasome subunit alpha2 / Proteasome subunit alpha4 / Proteasome subunit alpha 1 / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit ...Proteasome subunit alpha2 / Proteasome subunit alpha4 / Proteasome subunit alpha 1 / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit alpha type ...Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit beta type-5 / Proteasome subunit alpha type-3
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsKandolf, S. / Grishkovskaya, I. / Meinhart, A. / Haselbach, D.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Plant Commun / Year: 2022
Title: Cryo-EM structure of the plant 26S proteasome.
Authors: Susanne Kandolf / Irina Grishkovskaya / Katarina Belačić / Derek L Bolhuis / Sascha Amann / Brent Foster / Richard Imre / Karl Mechtler / Alexander Schleiffer / Hemant D Tagare / Ellen D ...Authors: Susanne Kandolf / Irina Grishkovskaya / Katarina Belačić / Derek L Bolhuis / Sascha Amann / Brent Foster / Richard Imre / Karl Mechtler / Alexander Schleiffer / Hemant D Tagare / Ellen D Zhong / Anton Meinhart / Nicholas G Brown / David Haselbach /
Abstract: Targeted proteolysis is a hallmark of life. It is especially important in long-lived cells that can be found in higher eukaryotes, like plants. This task is mainly fulfilled by the ubiquitin- ...Targeted proteolysis is a hallmark of life. It is especially important in long-lived cells that can be found in higher eukaryotes, like plants. This task is mainly fulfilled by the ubiquitin-proteasome system. Thus, proteolysis by the 26S proteasome is vital to development, immunity, and cell division. Although the yeast and animal proteasomes are well characterized, there is only limited information on the plant proteasome. We determined the first plant 26S proteasome structure from Spinacia oleracea by single-particle electron cryogenic microscopy at an overall resolution of 3.3 Å. We found an almost identical overall architecture of the spinach proteasome compared with the known structures from mammals and yeast. Nevertheless, we noticed a structural difference in the proteolytic active β1 subunit. Furthermore, we uncovered an unseen compression state by characterizing the proteasome's conformational landscape. We suspect that this new conformation of the 20S core protease, in correlation with a partial opening of the unoccupied gate, may contribute to peptide release after proteolysis. Our data provide a structural basis for the plant proteasome, which is crucial for further studies.
History
DepositionJan 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
i: Proteasome subunit alpha type
j: Proteasome subunit alpha type
k: Proteasome subunit alpha type
l: Proteasome subunit alpha type
m: Proteasome subunit alpha type
n: Proteasome subunit alpha type-3
B: Proteasome subunit alpha type
C: Proteasome subunit alpha type
D: Proteasome subunit alpha type
E: Proteasome subunit alpha type
F: Proteasome subunit alpha type
G: Proteasome subunit alpha type
X: Proteasome subunit alpha type-3
o: Proteasome subunit beta
p: Proteasome subunit beta
q: Proteasome subunit beta
r: Proteasome subunit beta
s: Proteasome subunit beta type-5
t: Proteasome subunit beta
u: Proteasome subunit beta
a: Proteasome subunit beta
b: Proteasome subunit beta
c: Proteasome subunit beta
d: Proteasome subunit beta
e: Proteasome subunit beta type-5
f: Proteasome subunit beta
g: Proteasome subunit beta
h: Proteasome subunit alpha type


Theoretical massNumber of molelcules
Total (without water)745,08628
Polymers745,08628
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area111350 Å2
ΔGint-412 kcal/mol
Surface area210430 Å2

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Components

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Proteasome subunit ... , 14 types, 28 molecules iCjDkElFmGnXBhoapbqcrdsetfug

#1: Protein Proteasome subunit alpha type /


Mass: 25588.023 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QA79
#2: Protein Proteasome subunit alpha type /


Mass: 27504.117 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RH20
#3: Protein Proteasome subunit alpha type /


Mass: 26844.439 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9S0K6
#4: Protein Proteasome subunit alpha type /


Mass: 26027.238 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RE77
#5: Protein Proteasome subunit alpha type /


Mass: 29932.393 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RGG6
#6: Protein Proteasome subunit alpha type-3 / / 20S proteasome alpha subunit G / 20S proteasome subunit alpha-7 / Proteasome component C8


Mass: 27322.258 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: O24362
#7: Protein Proteasome subunit alpha type /


Mass: 27211.789 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R8Z8
#8: Protein Proteasome subunit beta /


Mass: 25324.434 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9S2G1
#9: Protein Proteasome subunit beta /


Mass: 29404.385 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9S3A8
#10: Protein Proteasome subunit beta /


Mass: 22847.109 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9S024
#11: Protein Proteasome subunit beta /


Mass: 22950.082 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QSM9
#12: Protein Proteasome subunit beta type-5 / PSMB5 / 20S proteasome subunit E / Proteasome epsilon chain


Mass: 29652.654 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach)
References: UniProt: O24361, proteasome endopeptidase complex
#13: Protein Proteasome subunit beta /


Mass: 24835.199 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RTN8
#14: Protein Proteasome subunit beta /


Mass: 27098.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RED8

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Spinach 26S proteasome / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 1.7 MDa / Experimental value: YES
Source (natural)Organism: Spinacia oleracea (spinach)
Buffer solutionpH: 6.5
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMbis(2-hydroxyethyl)amino-tris(hydroxymethyl)methanBis-TrisBis-tris methane1
250 mMpotassium chlorideKCl1
35 mMmagnedium chlorideMgCl21
45 %glycerolglycerol1
520 mMadenosine triphosphateATPAdenosine triphosphate1
65 mMdithiothreitolDTT1
75 %polyvinylpolypyrrolidonePVP1
82 mMphenylmethylsulfonyl fluoridePMSFPMSF1
SpecimenConc.: 0.02 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R3.5/1
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: 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 holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recording
IDImaging-IDElectron dose (e/Å2)Detector modeFilm or detector modelNum. of real images
1180INTEGRATINGFEI FALCON III (4k x 4k)24769
2150INTEGRATINGFEI FALCON III (4k x 4k)8089
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3particle selection
2EPUimage acquisition
4cryoSPARC3CTF correction
7UCSF Chimera8.6.9model fitting
8Coot0.9.5model fitting
10PHENIX1.18.2model refinement
11cryoSPARC3initial Euler assignment
12cryoSPARC3final Euler assignment
13cryoSPARC3classification
14cryoSPARC33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 951422
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 951422 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingB value: 109.9 / Protocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 6MSB

6msb

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