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- PDB-7e55: Cryo-EM structure of alpha 7 homo-tetradecamer -

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Entry
Database: PDB / ID: 7.0E+55
TitleCryo-EM structure of alpha 7 homo-tetradecamer
ComponentsProteasome subunit alpha type-3
KeywordsLYASE / Conformational fluctuation / double-ring / proteasome / D7 symmetry / CHAPERONE
Function / homology
Function and homology information


regulation of endopeptidase activity / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / negative regulation of G2/M transition of mitotic cell cycle / Wnt signaling pathway, planar cell polarity pathway / NIK/NF-kappaB signaling / proteasomal ubiquitin-independent protein catabolic process / proteasome complex / proteasome core complex ...regulation of endopeptidase activity / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / negative regulation of G2/M transition of mitotic cell cycle / Wnt signaling pathway, planar cell polarity pathway / NIK/NF-kappaB signaling / proteasomal ubiquitin-independent protein catabolic process / proteasome complex / proteasome core complex / regulation of hematopoietic stem cell differentiation / regulation of mitotic cell cycle phase transition / proteasome core complex, alpha-subunit complex / regulation of cellular amino acid metabolic process / Regulation of activated PAK-2p34 by proteasome mediated degradation / CDT1 association with the CDC6:ORC:origin complex / Degradation of DVL / pre-replicative complex assembly / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Ubiquitin-dependent degradation of Cyclin D / Vif-mediated degradation of APOBEC3G / Defective CFTR causes cystic fibrosis / Hedgehog ligand biogenesis / Vpu mediated degradation of CD4 / AUF1 (hnRNP D0) binds and destabilizes mRNA / Degradation of GLI1 by the proteasome / TNFR2 non-canonical NF-kB pathway / Negative regulation of NOTCH4 signaling / Dectin-1 mediated noncanonical NF-kB signaling / Hedgehog 'on' state / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / ABC-family proteins mediated transport / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Activation of NF-kappaB in B cells / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / GLI3 is processed to GLI3R by the proteasome / Degradation of GLI2 by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of AXIN / G2/M Checkpoints / tumor necrosis factor-mediated signaling pathway / Autodegradation of the E3 ubiquitin ligase COP1 / Degradation of beta-catenin by the destruction complex / Regulation of RUNX3 expression and activity / Regulation of expression of SLITs and ROBOs / MAPK6/MAPK4 signaling / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Regulation of RAS by GAPs / regulation of transcription from RNA polymerase II promoter in response to hypoxia / Interleukin-1 signaling / CDK-mediated phosphorylation and removal of Cdc6 / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent / UCH proteinases / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / interleukin-1-mediated signaling pathway / Orc1 removal from chromatin / FCERI mediated NF-kB activation / Separation of Sister Chromatids / Regulation of RUNX2 expression and activity / Regulation of PTEN stability and activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of canonical Wnt signaling pathway / Neddylation / negative regulation of canonical Wnt signaling pathway / The role of GTSE1 in G2/M progression after G2 checkpoint / anaphase-promoting complex-dependent catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / RUNX1 regulates transcription of genes involved in differentiation of HSCs / stimulatory C-type lectin receptor signaling pathway / regulation of mRNA stability / Downstream TCR signaling / Fc-epsilon receptor signaling pathway / transmembrane transport / ER-Phagosome pathway / post-translational protein modification / protein polyubiquitination / T cell receptor signaling pathway / endopeptidase activity / Ub-specific processing proteases / protein deubiquitination / MAPK cascade / synapse / ubiquitin protein ligase binding / viral process / extracellular exosome / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Proteasome subunit alpha 3 / Proteasome alpha-type subunits signature. / Proteasome subunit A N-terminal signature / Proteasome subunit A N-terminal signature Add an annotation / Proteasome alpha-subunit, N-terminal domain / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
Proteasome subunit alpha type-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.9 Å
AuthorsSong, C. / Murata, K.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP19K16088 Japan
Japan Society for the Promotion of Science (JSPS)JP18H05229 Japan
Japan Society for the Promotion of Science (JSPS)JP18H05534 Japan
Japan Society for the Promotion of Science (JSPS)JP18H03681 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP16H06280 Japan
CitationJournal: Int J Mol Sci / Year: 2021
Title: Structural Fluctuations of the Human Proteasome α7 Homo-Tetradecamer Double Ring Imply the Proteasomal α-Ring Assembly Mechanism.
Authors: Chihong Song / Tadashi Satoh / Taichiro Sekiguchi / Koichi Kato / Kazuyoshi Murata /
Abstract: The 20S proteasome, which is composed of layered α and β heptameric rings, is the core complex of the eukaryotic proteasome involved in proteolysis. The α7 subunit is a component of the α ring, ...The 20S proteasome, which is composed of layered α and β heptameric rings, is the core complex of the eukaryotic proteasome involved in proteolysis. The α7 subunit is a component of the α ring, and it self-assembles into a homo-tetradecamer consisting of two layers of α7 heptameric rings. However, the structure of the α7 double ring in solution has not been fully elucidated. We applied cryo-electron microscopy to delineate the structure of the α7 double ring in solution, revealing a structure different from the previously reported crystallographic model. The D7-symmetrical double ring was stacked with a 15° clockwise twist and a separation of 3 Å between the two rings. Two more conformations, dislocated and fully open, were also identified. Our observations suggest that the α7 double-ring structure fluctuates considerably in solution, allowing for the insertion of homologous α subunits, finally converting to the hetero-heptameric α rings in the 20S proteasome.
History
DepositionFeb 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

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Assembly

Deposited unit
A: Proteasome subunit alpha type-3


Theoretical massNumber of molelcules
Total (without water)28,4691
Polymers28,4691
Non-polymers00
Water0
1
A: Proteasome subunit alpha type-3
x 14


Theoretical massNumber of molelcules
Total (without water)398,57014
Polymers398,57014
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation14
2


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: D7 (2回x7回 2面回転対称))

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Components

#1: Protein Proteasome subunit alpha type-3 / / Macropain subunit C8 / Multicatalytic endopeptidase complex subunit C8 / Proteasome component C8


Mass: 28469.252 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA3, HC8, PSC8 / Production host: Escherichia coli (E. coli) / References: UniProt: P25788

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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: Proteasome subunit alpha type-7 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 1 mg/ml / Embedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: MOLYBDENUM / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
EM embeddingMaterial: Ice
VitrificationCryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: JEOL 2200FS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 40000 X / Calibrated magnification: 45065 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 4.2 mm / C2 aperture diameter: 40 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN
Model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Temperature (max): 77 K / Temperature (min): 76 K
Image recordingAverage exposure time: 5 sec. / Electron dose: 40 e/Å2 / Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k)
EM imaging opticsEnergyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV
Image scansSampling size: 6.4 µm / Width: 5120 / Height: 3840 / Movie frames/image: 25

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
2RELION3.1image acquisition
4CTFFIND4CTF correction
7PHENIXmodel fitting
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
12RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: D7 (2回x7回 2面回転対称)
3D reconstructionResolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18388 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingB value: 531 / Protocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 5DSV
Pdb chain residue range: 2-245

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