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- PDB-7drw: Bovine 20S immunoproteasome in complex with two human PA28alpha-b... -

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Entry
Database: PDB / ID: 7drw
TitleBovine 20S immunoproteasome in complex with two human PA28alpha-beta activators
Components
  • (Proteasome activator complex subunit ...) x 2
  • (Proteasome subunit alpha type- ...) x 7
  • (Proteasome subunit beta type- ...) x 7
KeywordsHYDROLASE / proteasome / immunoproteasome / bovine spleen / PA28
Function / homology
Function and homology information


Cross-presentation of soluble exogenous antigens (endosomes) / Regulation of ornithine decarboxylase (ODC) / proteasome activator complex / spermatoproteasome complex / 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 ...Cross-presentation of soluble exogenous antigens (endosomes) / Regulation of ornithine decarboxylase (ODC) / proteasome activator complex / spermatoproteasome complex / 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 and presentation of exogenous antigen / UCH proteinases / Antigen processing: Ubiquitination & Proteasome degradation / 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 / Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Neutrophil degranulation / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / immune system process / fat cell differentiation / regulation of G1/S transition of mitotic cell cycle / endopeptidase activator activity / antigen processing and presentation / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / regulation of proteasomal protein catabolic process / negative regulation of inflammatory response to antigenic stimulus / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / proteasome complex / proteolysis involved in protein catabolic process / Regulation of activated PAK-2p34 by proteasome mediated degradation / ciliary basal body / 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 / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Degradation of DVL / proteasomal protein catabolic process / P-body / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Degradation of AXIN / Defective CFTR causes cystic fibrosis / Degradation of GLI1 by the proteasome / lipopolysaccharide binding / Activation of NF-kappaB in B cells / Hedgehog ligand biogenesis / Negative regulation of NOTCH4 signaling / G2/M Checkpoints / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state
Similarity search - Function
Proteasome activator PA28, N-terminal domain / Proteasome activator PA28, N-terminal domain superfamily / Proteasome activator pa28 alpha subunit / Proteasome activator PA28 / Proteasome activator PA28, C-terminal domain / Proteasome activator superfamily / Proteasome activator PA28, C-terminal domain superfamily / Proteasome activator pa28 beta subunit / Proteasome subunit alpha 1 / Proteasome beta subunit, C-terminal ...Proteasome activator PA28, N-terminal domain / Proteasome activator PA28, N-terminal domain superfamily / Proteasome activator pa28 alpha subunit / Proteasome activator PA28 / Proteasome activator PA28, C-terminal domain / Proteasome activator superfamily / Proteasome activator PA28, C-terminal domain superfamily / Proteasome activator pa28 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 activator complex subunit 1 / 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 beta type-3 / Proteasome activator complex subunit 1 / 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 / Proteasome activator complex subunit 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsCong, Y. / Xu, C.
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 29, 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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  • EMDB-30828
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Assembly

Deposited unit
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 activator complex subunit 2
I: Proteasome activator complex subunit 1
J: Proteasome activator complex subunit 1
K: Proteasome activator complex subunit 2
L: Proteasome activator complex subunit 1
M: Proteasome activator complex subunit 2
N: Proteasome activator complex subunit 1
O: Proteasome activator complex subunit 2
Q: Proteasome activator complex subunit 1
a: Proteasome activator complex subunit 1
c: Proteasome activator complex subunit 2
e: Proteasome activator complex subunit 1
g: Proteasome activator complex subunit 2
i: Proteasome activator complex subunit 1
P: Proteasome subunit alpha type-7
R: Proteasome subunit alpha type-5
b: Proteasome subunit alpha type-1
d: Proteasome subunit alpha type-3
f: Proteasome subunit alpha type-6
h: Proteasome subunit alpha type-2
j: Proteasome subunit alpha type-4
k: Proteasome subunit beta type-3
l: Proteasome subunit beta type-2
m: Proteasome subunit beta type-1
n: Proteasome subunit beta type-4
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)1,153,41142
Polymers1,153,41142
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area173920 Å2
ΔGint-721 kcal/mol
Surface area358330 Å2

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Components

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

#1: 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
#2: 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 (cattle) / References: UniProt: Q3T0Y5
#3: 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
#4: 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 (cattle) / References: UniProt: Q3ZBG0
#5: 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 (cattle) / References: UniProt: Q5E987
#6: 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 (cattle) / References: UniProt: Q3T0X5
#7: 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 (cattle) / References: UniProt: Q58DU5

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Proteasome activator complex subunit ... , 2 types, 14 molecules HKMOcgIJLNQaei

#8: Protein
Proteasome activator complex subunit 2 / 11S regulator complex subunit beta / REG-beta / Activator of multicatalytic protease subunit 2 / ...11S regulator complex subunit beta / REG-beta / Activator of multicatalytic protease subunit 2 / Proteasome activator 28 subunit beta / PA28beta


Mass: 27398.600 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSME2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UL46
#9: Protein
Proteasome activator complex subunit 1 / 11S regulator complex subunit alpha / REG-alpha / Activator of multicatalytic protease subunit 1 / ...11S regulator complex subunit alpha / REG-alpha / Activator of multicatalytic protease subunit 1 / Interferon gamma up-regulated I-5111 protein / IGUP I-5111 / Proteasome activator 28 subunit alpha / PA28alpha


Mass: 28768.141 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSME1, IFI5111 / Production host: Escherichia coli (E. coli) / References: UniProt: Q06323

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Proteasome subunit beta type- ... , 7 types, 14 molecules kSlTmUnVWZX1Y2

#10: Protein Proteasome subunit beta type-3 / PSMB3 / 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 (cattle)
References: UniProt: P33672, proteasome endopeptidase complex
#11: Protein Proteasome subunit beta type-2 / PSMB2


Mass: 22924.309 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
References: UniProt: Q5E9K0, proteasome endopeptidase complex
#12: Protein Proteasome subunit beta type-1 / PSMB1


Mass: 26278.059 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
References: UniProt: Q2TBX6, proteasome endopeptidase complex
#13: Protein Proteasome subunit beta type-4 / PSMB4


Mass: 29057.018 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
References: UniProt: Q3T108, proteasome endopeptidase complex
#14: 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 (cattle)
References: UniProt: Q3SZC2, proteasome endopeptidase complex
#15: 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 (cattle)
References: UniProt: Q3T0T1, proteasome endopeptidase complex
#16: 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 (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 (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 FIELDBright-field microscopy
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: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24657 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00272960
ELECTRON MICROSCOPYf_angle_d0.52398588
ELECTRON MICROSCOPYf_dihedral_angle_d5.6961132
ELECTRON MICROSCOPYf_chiral_restr0.0411127
ELECTRON MICROSCOPYf_plane_restr0.00412715

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