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- PDB-8azk: Bovine 20S proteasome, untreated -

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Basic information

Entry
Database: PDB / ID: 8azk
TitleBovine 20S proteasome, untreated
Components
  • (Proteasome subunit alpha type- ...) x 7
  • (Proteasome subunit beta type- ...) x 7
KeywordsHYDROLASE / 20S proteasome / Degradation / Proteolysis
Function / homology
Function and homology information


Cross-presentation of soluble exogenous antigens (endosomes) / Regulation of ornithine decarboxylase (ODC) / Activation of NF-kappaB in B cells / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / Autodegradation of the E3 ubiquitin ligase COP1 ...Cross-presentation of soluble exogenous antigens (endosomes) / Regulation of ornithine decarboxylase (ODC) / Activation of NF-kappaB in B cells / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / Autodegradation of the E3 ubiquitin ligase COP1 / Asymmetric localization of PCP proteins / Degradation of AXIN / Degradation of DVL / Hedgehog ligand biogenesis / Dectin-1 mediated noncanonical NF-kB signaling / CLEC7A (Dectin-1) signaling / Degradation of GLI1 by the proteasome / Hedgehog 'on' state / TNFR2 non-canonical NF-kB pathway / NIK-->noncanonical NF-kB signaling / Assembly of the pre-replicative complex / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / G2/M Checkpoints / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Regulation of RUNX2 expression and activity / Regulation of RUNX3 expression and activity / Regulation of PTEN stability and activity / Interleukin-1 signaling / KEAP1-NFE2L2 pathway / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Degradation of beta-catenin by the destruction complex / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / UCH proteinases / ABC-family proteins mediated transport / Ub-specific processing proteases / Downstream TCR signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / AUF1 (hnRNP D0) binds and destabilizes mRNA / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / proteasome core complex / Neutrophil degranulation / immune system process / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / negative regulation of inflammatory response to antigenic stimulus / ciliary basal body / proteolysis involved in protein catabolic process / lipopolysaccharide binding / P-body / postsynapse / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / response to oxidative stress / centrosome / synapse / mitochondrion / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Proteasome subunit alpha 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / 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 alpha 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / 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 beta type-3 / Proteasome subunit beta type-7 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-6 / Proteasome subunit beta type-5 / Proteasome subunit beta type-6 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-7 ...Proteasome subunit beta type-3 / Proteasome subunit beta type-7 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-6 / Proteasome subunit beta type-5 / Proteasome subunit beta type-6 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-7 / Proteasome subunit alpha type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-2
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSzenkier, N. / Arie, M. / Matzov, D. / Sertchook, R. / Carmeli, R. / Cascio, P. / Stanhill, A. / Shalev Benami, M. / Navon, A.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation Israel
CitationJournal: To be published
Title: Bovine 20S proteasome, untreated
Authors: Szenkier, N. / Arie, M. / Matzov, D. / Sertchook, R. / Carmeli, R. / Cascio, P. / Stanhill, A. / Shalev Benami, M. / Navon, A.
History
DepositionSep 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
J: Proteasome subunit beta type-3
X: Proteasome subunit beta type-3
A: Proteasome subunit alpha type-6
B: Proteasome subunit alpha type-2
C: Proteasome subunit alpha type-4
D: Proteasome subunit alpha type-7
E: Proteasome subunit alpha type-5
F: Proteasome subunit alpha type-1
G: Proteasome subunit alpha type-3
H: Proteasome subunit beta type-6
I: Proteasome subunit beta type-7
K: Proteasome subunit beta type-2
L: Proteasome subunit beta type-5
M: Proteasome subunit beta type-1
N: Proteasome subunit beta type-4
O: Proteasome subunit alpha type-6
P: Proteasome subunit alpha type-2
Q: Proteasome subunit alpha type-4
R: Proteasome subunit alpha type-7
S: Proteasome subunit alpha type-5
T: Proteasome subunit alpha type-1
U: Proteasome subunit alpha type-3
V: Proteasome subunit beta type-6
W: Proteasome subunit beta type-7
Y: Proteasome subunit beta type-2
Z: Proteasome subunit beta type-5
1: Proteasome subunit beta type-1
2: Proteasome subunit beta type-4


Theoretical massNumber of molelcules
Total (without water)717,34128
Polymers717,34128
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, negative stain, light scattering, mass photometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area99200 Å2
ΔGint-397 kcal/mol
Surface area236850 Å2
MethodPISA

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Components

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Proteasome subunit beta type- ... , 7 types, 14 molecules JXHVIWKYLZM1N2

#1: Protein Proteasome subunit beta type-3 / Proteasome chain 13 / Proteasome component C10-II / Proteasome theta chain


Mass: 22954.859 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P33672
#9: Protein Proteasome subunit beta type-6


Mass: 21921.836 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
References: UniProt: Q3MHN0, proteasome endopeptidase complex
#10: Protein Proteasome subunit beta type-7


Mass: 25351.047 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
References: UniProt: Q2TBP0, proteasome endopeptidase complex
#11: Protein Proteasome subunit beta type-2


Mass: 22864.277 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q5E9K0
#12: Protein Proteasome subunit beta type-5


Mass: 22484.369 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
References: UniProt: Q32KL2, proteasome endopeptidase complex
#13: Protein Proteasome subunit beta type-1


Mass: 23578.986 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q2TBX6
#14: Protein Proteasome subunit beta type-4


Mass: 24402.686 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3T108

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Proteasome subunit alpha type- ... , 7 types, 14 molecules AOBPCQDRESFTGU

#2: Protein Proteasome subunit alpha type-6


Mass: 27432.459 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q2YDE4
#3: Protein Proteasome subunit alpha type-2


Mass: 25796.338 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3T0Y5
#4: Protein Proteasome subunit alpha type-4


Mass: 29525.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3ZCK9
#5: Protein Proteasome subunit alpha type-7


Mass: 27929.891 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3ZBG0
#6: Protein Proteasome subunit alpha type-5


Mass: 26494.016 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q5E987
#7: Protein Proteasome subunit alpha type-1


Mass: 29595.627 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3T0X5
#8: Protein Proteasome subunit alpha type-3


Mass: 28338.057 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q58DU5

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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: Untreated 20S proteasome / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.7 MDa / Experimental value: YES
Source (natural)Organism: Bos taurus (cattle) / Organ: Dyaphragma muscle
Buffer solutionpH: 7.5
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / 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: OTHER / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.19.2_4158refinement
PHENIX1.19.2_4158refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 346962 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 39.58 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004247846
ELECTRON MICROSCOPYf_angle_d0.759964849
ELECTRON MICROSCOPYf_chiral_restr0.04877420
ELECTRON MICROSCOPYf_plane_restr0.00518349
ELECTRON MICROSCOPYf_dihedral_angle_d16.955717138

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