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- PDB-8amz: Spinach 19S proteasome -

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Basic information

Entry
Database: PDB / ID: 8amz
TitleSpinach 19S proteasome
Components
  • (26S proteasome non-ATPase regulatory subunit ...) x 2
  • (26S proteasome regulatory subunit ...) x 2
  • (AAA domain-containing ...) x 5
  • (PCI domain-containing ...) x 6
  • MPN domain-containing protein
  • VWFA domain-containing protein
KeywordsPLANT PROTEIN / PROTEASOME / UPS / PLANT / SPINACH
Function / homology
Function and homology information


: / : / nuclear proteasome complex / proteasome regulatory particle / cytosolic proteasome complex / proteasome-activating activity / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / metal-dependent deubiquitinase activity / K63-linked deubiquitinase activity ...: / : / nuclear proteasome complex / proteasome regulatory particle / cytosolic proteasome complex / proteasome-activating activity / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / metal-dependent deubiquitinase activity / K63-linked deubiquitinase activity / proteasome binding / regulation of protein catabolic process / proteasome storage granule / polyubiquitin modification-dependent protein binding / protein deubiquitination / positive regulation of RNA polymerase II transcription preinitiation complex assembly / membrane => GO:0016020 / enzyme regulator activity / proteasome complex / metallopeptidase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / structural molecule activity / ATP hydrolysis activity / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
26S Proteasome non-ATPase regulatory subunit 14 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #570 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #990 / 26S proteasome regulatory subunit P45-like / 26S Proteasome regulatory subunit 6B / 26S proteasome regulatory subunit 8 / Cytidine Deaminase, domain 2 / Ubiquitin interaction motif / Cytidine Deaminase; domain 2 / 26S proteasome non-ATPase regulatory subunit Rpn12 ...26S Proteasome non-ATPase regulatory subunit 14 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #570 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #990 / 26S proteasome regulatory subunit P45-like / 26S Proteasome regulatory subunit 6B / 26S proteasome regulatory subunit 8 / Cytidine Deaminase, domain 2 / Ubiquitin interaction motif / Cytidine Deaminase; domain 2 / 26S proteasome non-ATPase regulatory subunit Rpn12 / 26S proteasome regulatory subunit, C-terminal / Proteasome regulatory subunit C-terminal / 26S proteasome regulatory subunit RPN5, C-terminal domain / 26S proteasome regulatory subunit RPN5 C-terminal domain / 26S proteasome regulatory subunit Rpn6, N-terminal / 6S proteasome subunit Rpn6, C-terminal helix domain / 26S proteasome regulatory subunit RPN6 N-terminal domain / 26S proteasome subunit RPN6 C-terminal helix domain / 26S Proteasome non-ATPase regulatory subunit 13 / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / 26S proteasome regulatory subunit RPN2, C-terminal / 26S proteasome regulatory subunit RPN2 C-terminal domain / 26S Proteasome non-ATPase regulatory subunit 7/8 / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / RPN1, N-terminal / 26S proteasome non-ATPase regulatory subunit RPN1, C-terminal / RPN1 N-terminal domain / 26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / : / 26S proteasome regulatory subunit 7, OB domain / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 26S proteasome regulatory subunit Rpn7, N-terminal / 26S proteasome subunit RPN7 / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / Proteasome/cyclosome repeat / Ubiquitin-interacting motif. / Proteasome/cyclosome repeat / : / von Willebrand factor type A domain / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / Helicase, Ruva Protein; domain 3 - #60 / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Leucine-rich Repeat Variant / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Leucine-rich Repeat Variant / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / AAA ATPase, AAA+ lid domain / AAA+ lid domain / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / ATPase, AAA-type, conserved site / AAA-protein family signature. / Helicase, Ruva Protein; domain 3 / von Willebrand factor A-like domain superfamily / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Winged helix DNA-binding domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / PCI domain-containing protein / AAA domain-containing protein / MPN domain-containing protein / AAA domain-containing protein / VWFA domain-containing protein / AAA domain-containing protein / AAA domain-containing protein / PCI domain-containing protein ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / PCI domain-containing protein / AAA domain-containing protein / MPN domain-containing protein / AAA domain-containing protein / VWFA domain-containing protein / AAA domain-containing protein / AAA domain-containing protein / PCI domain-containing protein / PCI domain-containing protein / PCI domain-containing protein / 26S proteasome non-ATPase regulatory subunit 2 homolog / 26S proteasome non-ATPase regulatory subunit 1 homolog / PCI domain-containing protein / PCI domain-containing protein / AAA domain-containing protein / MPN domain-containing protein / 26S proteasome regulatory subunit 7
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 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
DepositionAug 4, 2022Deposition site: PDBE / Processing site: PDBE
SupersessionAug 24, 2022ID: 7QVG
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: 26S proteasome regulatory subunit 7
I: AAA domain-containing protein
J: AAA domain-containing protein
K: AAA domain-containing protein
L: AAA domain-containing protein
M: AAA domain-containing protein
V: 26S proteasome regulatory subunit RPN11
S: PCI domain-containing protein
T: PCI domain-containing protein
W: VWFA domain-containing protein
O: PCI domain-containing protein
U: MPN domain-containing protein
Q: PCI domain-containing protein
P: PCI domain-containing protein
Z: 26S proteasome non-ATPase regulatory subunit 2 homolog
N: 26S proteasome non-ATPase regulatory subunit 1 homolog
R: PCI domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)875,72219
Polymers874,78717
Non-polymers9342
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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26S proteasome regulatory subunit ... , 2 types, 2 molecules HV

#1: Protein 26S proteasome regulatory subunit 7 / 26S proteasome AAA-ATPase subunit RPT1 / 26S proteasome subunit 7 / Regulatory particle triple-A ...26S proteasome AAA-ATPase subunit RPT1 / 26S proteasome subunit 7 / Regulatory particle triple-A ATPase subunit 1


Mass: 47786.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q41365
#7: Protein 26S proteasome regulatory subunit RPN11


Mass: 34506.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QHF5

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AAA domain-containing ... , 5 types, 5 molecules IJKLM

#2: Protein AAA domain-containing protein


Mass: 49635.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QMF8
#3: Protein AAA domain-containing 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 AAA domain-containing 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 AAA domain-containing 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 AAA domain-containing protein


Mass: 47754.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QR38

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PCI domain-containing ... , 6 types, 6 molecules STOQPR

#8: Protein PCI domain-containing protein


Mass: 55356.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R856
#9: Protein PCI domain-containing 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 PCI domain-containing 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 PCI domain-containing 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 PCI domain-containing 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 PCI domain-containing protein


Mass: 44432.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QVX1

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Protein , 2 types, 2 molecules WU

#10: Protein VWFA domain-containing protein


Mass: 42562.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QPY6
#12: Protein MPN domain-containing protein


Mass: 34457.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RYG8

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26S proteasome non-ATPase regulatory subunit ... , 2 types, 2 molecules ZN

#15: Protein 26S proteasome non-ATPase regulatory subunit 2 homolog


Mass: 98484.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RA51
#16: Protein 26S proteasome non-ATPase regulatory subunit 1 homolog


Mass: 109199.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RNX4

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Non-polymers , 2 types, 2 molecules

#18: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#19: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Details

Has ligand of interestN

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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: #1-#17 / 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-Tris1
250 mMpotassium chlorideKCl1
35 mMmagnedium chlorideMgCl21
45 %glycerolglycerol1
520 mMadenosine triphosphateATP1
65 mMdithiothreitolDTT1
75 %polyvinylpolypyrrolidonePVP1
82 mMphenylmethylsulfonyl fluoridePMSF1
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 FIELD / 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

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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


Accession code: 6MSB / Source name: PDB / Type: experimental model

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