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- PDB-7dr7: bovine 20S immunoproteasome -

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Basic information

Entry
Database: PDB / ID: 7dr7
Titlebovine 20S immunoproteasome
Components
  • (Proteasome subunit alpha type- ...) x 7
  • (Proteasome subunit beta type- ...) x 7
KeywordsHYDROLASE / proteasome / immunoproteasome / bovine spleen
Function / homology
Function and homology information


Cross-presentation of soluble exogenous antigens (endosomes) / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / spermatoproteasome complex / 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 / Autodegradation of the E3 ubiquitin ligase COP1 / Asymmetric localization of PCP proteins ...Cross-presentation of soluble exogenous antigens (endosomes) / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / spermatoproteasome complex / 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 / Autodegradation of the E3 ubiquitin ligase COP1 / Asymmetric localization of PCP proteins / Degradation of AXIN / Degradation of DVL / Hedgehog ligand biogenesis / Hedgehog 'on' state / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / G2/M Checkpoints / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Regulation of RUNX3 expression and activity / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / Activation of NF-kappaB in B cells / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / Dectin-1 mediated noncanonical NF-kB signaling / CLEC7A (Dectin-1) signaling / Degradation of GLI1 by the proteasome / NIK-->noncanonical NF-kB signaling / Orc1 removal from chromatin / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Regulation of RUNX2 expression and activity / Interleukin-1 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / 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 / AUF1 (hnRNP D0) binds and destabilizes mRNA / Separation of Sister Chromatids / MAPK6/MAPK4 signaling / GLI3 is processed to GLI3R by the proteasome / Neutrophil degranulation / proteasome core complex / fat cell differentiation / immune system process / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteolysis involved in protein catabolic process / ciliary basal body / negative regulation of inflammatory response to antigenic stimulus / lipopolysaccharide binding / P-body / endopeptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / synapse / mitochondrion / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Proteasome subunit alpha 1 / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 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 subunit alpha 1 / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 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 B-type subunit / Proteasome beta-type subunit profile. / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Proteasome subunit beta type-3 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-6 / Proteasome subunit beta type-9 / Proteasome subunit beta type-10 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-4 / Proteasome subunit beta type-8 / Proteasome subunit alpha type-7 ...Proteasome subunit beta type-3 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-6 / Proteasome subunit beta type-9 / Proteasome subunit beta type-10 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-4 / Proteasome subunit beta type-8 / 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 (domestic cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsXu, C. / Cong, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Nat Commun / Year: 2021
Title: Cryo-EM of mammalian PA28αβ-iCP immunoproteasome reveals a distinct mechanism of proteasome activation by PA28αβ.
Authors: Jinhuan Chen / Yifan Wang / Cong Xu / Kaijian Chen / Qiaoyu Zhao / Shutian Wang / Yue Yin / Chao Peng / Zhanyu Ding / Yao Cong /
Abstract: The proteasome activator PA28αβ affects MHC class I antigen presentation by associating with immunoproteasome core particles (iCPs). However, due to the lack of a mammalian PA28αβ-iCP structure, ...The proteasome activator PA28αβ affects MHC class I antigen presentation by associating with immunoproteasome core particles (iCPs). However, due to the lack of a mammalian PA28αβ-iCP structure, how PA28αβ regulates proteasome remains elusive. Here we present the complete architectures of the mammalian PA28αβ-iCP immunoproteasome and free iCP at near atomic-resolution by cryo-EM, and determine the spatial arrangement between PA28αβ and iCP through XL-MS. Our structures reveal a slight leaning of PA28αβ towards the α3-α4 side of iCP, disturbing the allosteric network of the gatekeeper α2/3/4 subunits, resulting in a partial open iCP gate. We find that the binding and activation mechanism of iCP by PA28αβ is distinct from those of constitutive CP by the homoheptameric TbPA26 or PfPA28. Our study sheds lights on the mechanism of enzymatic activity stimulation of immunoproteasome and suggests that PA28αβ-iCP has experienced profound remodeling during evolution to achieve its current level of function in immune response.
History
DepositionDec 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Proteasome subunit alpha type-7
B: Proteasome subunit alpha type-5
C: Proteasome subunit alpha type-1
D: Proteasome subunit alpha type-3
E: Proteasome subunit alpha type-6
F: Proteasome subunit alpha type-2
G: Proteasome subunit alpha type-4
H: Proteasome subunit beta type-3
I: Proteasome subunit beta type-2
J: Proteasome subunit beta type-1
K: Proteasome subunit beta type-4
L: Proteasome subunit alpha type-6
M: Proteasome subunit alpha type-2
N: Proteasome subunit alpha type-4
O: Proteasome subunit alpha type-7
P: Proteasome subunit alpha type-5
Q: Proteasome subunit alpha type-1
R: Proteasome subunit alpha type-3
S: Proteasome subunit beta type-3
T: Proteasome subunit beta type-2
U: Proteasome subunit beta type-1
V: Proteasome subunit beta type-4
W: Proteasome subunit beta type-9
X: Proteasome subunit beta type-10
Y: Proteasome subunit beta type-8
Z: Proteasome subunit beta type-9
1: Proteasome subunit beta type-10
2: Proteasome subunit beta type-8


Theoretical massNumber of molelcules
Total (without water)758,87428
Polymers758,87428
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area110850 Å2
ΔGint-436 kcal/mol
Surface area225920 Å2

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Components

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

#1: Protein Proteasome subunit alpha type-7


Mass: 27911.912 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q3ZBG0
#2: Protein Proteasome subunit alpha type-5


Mass: 26435.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q5E987
#3: Protein Proteasome subunit alpha type-1


Mass: 29625.654 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q3T0X5
#4: Protein Proteasome subunit alpha type-3


Mass: 28441.197 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q58DU5
#5: 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 (domestic cattle) / References: UniProt: Q2YDE4
#6: Protein Proteasome subunit alpha type-2


Mass: 25927.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q3T0Y5
#7: 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 (domestic cattle) / References: UniProt: Q3ZCK9

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Proteasome subunit beta type- ... , 7 types, 14 molecules HSITJUKVWZX1Y2

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


Mass: 23016.947 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
References: UniProt: P33672, proteasome endopeptidase complex
#9: Protein Proteasome subunit beta type-2


Mass: 22924.309 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
References: UniProt: Q5E9K0, proteasome endopeptidase complex
#10: Protein Proteasome subunit beta type-1


Mass: 26278.059 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
References: UniProt: Q2TBX6, proteasome endopeptidase complex
#11: Protein Proteasome subunit beta type-4


Mass: 29057.018 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
References: UniProt: Q3T108, proteasome endopeptidase complex
#12: Protein Proteasome subunit beta type-9 / Proteasome subunit beta-1i


Mass: 23427.428 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
References: UniProt: Q3SZC2, proteasome endopeptidase complex
#13: Protein Proteasome subunit beta type-10 / Proteasome subunit beta-2i


Mass: 29128.318 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
References: UniProt: Q3T0T1, proteasome endopeptidase complex
#14: Protein Proteasome subunit beta type-8 / Proteasome subunit beta-5i


Mass: 30304.332 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
References: UniProt: Q3T112, proteasome endopeptidase complex

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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: 20S immunoproteasome purified from bovine spleen / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Bos taurus (domestic cattle)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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
Image recordingElectron dose: 38 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 56663 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00449201
ELECTRON MICROSCOPYf_angle_d0.59166496
ELECTRON MICROSCOPYf_dihedral_angle_d7.2529681
ELECTRON MICROSCOPYf_chiral_restr0.0447455
ELECTRON MICROSCOPYf_plane_restr0.0048592

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