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- EMDB-39565: canine immunoproteasome 20S subunit in complex with compound 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-39565
Titlecanine immunoproteasome 20S subunit in complex with compound 2
Map data
Sample
  • Complex: 20S immunoproteasome
    • Protein or peptide: x 13 types
  • Protein or peptide: x 1 types
  • Ligand: x 2 types
KeywordsInhibitor / Complex / Proteasome / HYDROLASE
Function / homology
Function and homology information


Activation of NF-kappaB in B cells / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Cross-presentation of soluble exogenous antigens (endosomes) / 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 / Degradation of beta-catenin by the destruction complex / Downstream TCR signaling ...Activation of NF-kappaB in B cells / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Cross-presentation of soluble exogenous antigens (endosomes) / 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 / Degradation of beta-catenin by the destruction complex / Downstream TCR signaling / Separation of Sister Chromatids / FCERI mediated NF-kB activation / Autodegradation of the E3 ubiquitin ligase COP1 / Regulation of ornithine decarboxylase (ODC) / ABC-family proteins mediated transport / AUF1 (hnRNP D0) binds and destabilizes mRNA / 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 / GLI3 is processed to GLI3R by the proteasome / Hedgehog 'on' state / Regulation of RAS by GAPs / NIK-->noncanonical NF-kB signaling / UCH proteinases / Ub-specific processing proteases / 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 / The role of GTSE1 in G2/M progression after G2 checkpoint / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Regulation of RUNX2 expression and activity / Regulation of RUNX3 expression and activity / Regulation of PTEN stability and activity / Neddylation / Interleukin-1 signaling / KEAP1-NFE2L2 pathway / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Antigen processing: Ubiquitination & Proteasome degradation / TNFR2 non-canonical NF-kB pathway / MAPK6/MAPK4 signaling / spermatoproteasome complex / proteasome core complex / immune system process / fat cell differentiation / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / threonine-type endopeptidase activity / T cell proliferation / proteolysis involved in protein catabolic process / P-body / response to virus / cell morphogenesis / ubiquitin-dependent protein catabolic process / postsynapse / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / 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. ...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 / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit beta ...Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit alpha type / Proteasome subunit alpha type / Proteasome subunit beta type-8
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsKashima A / Arai Y
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Bioorg Med Chem / Year: 2024
Title: Optimization of α-amido boronic acids via cryo-electron microscopy analysis: Discovery of a novel highly selective immunoproteasome subunit LMP7 (β5i)/LMP2 (β1i) dual inhibitor.
Authors: Yuuki Arai / Hiroaki Shitama / Masahito Yamagishi / Satoshi Ono / Akiko Kashima / Masahiro Hiraizumi / Naoki Tsuda / Koushirou Katayama / Kouji Tanaka / Yuzo Koda / Sayuka Kato / Kei Sakata ...Authors: Yuuki Arai / Hiroaki Shitama / Masahito Yamagishi / Satoshi Ono / Akiko Kashima / Masahiro Hiraizumi / Naoki Tsuda / Koushirou Katayama / Kouji Tanaka / Yuzo Koda / Sayuka Kato / Kei Sakata / Osamu Nureki / Hiroshi Miyazaki /
Abstract: The immunoproteasome subunit LMP7 (β5i)/LMP2 (β1i) dual blockade has been reported to suppress B cell differentiation and activation, suggesting that the dual inhibition of LMP7/LMP2 is a promising ...The immunoproteasome subunit LMP7 (β5i)/LMP2 (β1i) dual blockade has been reported to suppress B cell differentiation and activation, suggesting that the dual inhibition of LMP7/LMP2 is a promising approach for treating autoimmune diseases. In contrast, the inhibition of the constitutive proteasome subunit β5c correlates with cytotoxicity against non-immune cells. Therefore, LMP7/LMP2 dual inhibitors with high selectivity over β5c may be desirable for treating autoimmune diseases. In this study, we present the optimization and discovery of α-amido boronic acids using cryo-electron microscopy (cryo-EM). The exploitation of structural differences between the proteasome subunits led to the identification of a highly selective LMP7/LMP2 dual inhibitor 19. Molecular dynamics simulation based on cryo-EM structures of the proteasome subunits complexed with 19 explained the inhibitory activity profile. In mice immunized with 4-hydroxy-3-nitrophenylacetyl conjugated to ovalbumin, results indicate that 19 is orally bioavailable and shows promise as potential treatment for autoimmune diseases.
History
DepositionMar 24, 2024-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateJul 31, 2024-
Current statusJul 31, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39565.png

Downloads & links

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Map

FileDownload / File: emd_39565.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 352 pix.
= 292.16 Å		0.83 Å/pix.
x 352 pix.
= 292.16 Å		0.83 Å/pix.
x 352 pix.
= 292.16 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.024
Minimum - Maximum-0.10945945 - 0.20623939
Average (Standard dev.)0.00024407273 (±0.00688768)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 292.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39565_msk_1.map
Projections & Slices
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Half map: #2

Fileemd_39565_half_map_1.map
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Half map: #1

Fileemd_39565_half_map_2.map
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Sample components

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Entire : 20S immunoproteasome

EntireName: 20S immunoproteasome
Components
  • Complex: 20S immunoproteasome
    • Protein or peptide: Proteasome subunit beta
    • Protein or peptide: Proteasome subunit alpha type
    • Protein or peptide: Proteasome subunit alpha type
    • Protein or peptide: Proteasome subunit alpha type
    • Protein or peptide: Proteasome subunit alpha type
    • Protein or peptide: Proteasome subunit alpha type
    • Protein or peptide: Proteasome subunit beta
    • Protein or peptide: Proteasome subunit beta
    • Protein or peptide: Proteasome subunit beta
    • Protein or peptide: Proteasome subunit alpha type
    • Protein or peptide: Proteasome subunit beta
    • Protein or peptide: Proteasome subunit alpha type
    • Protein or peptide: Proteasome subunit beta
  • Protein or peptide: Proteasome subunit beta type-8
  • Ligand: [(2~{R},3~{R})-3-azanyl-4-oxidanyl-butan-2-yl]oxy-[(~{R})-cyclohexyl-[(1-cyclohexyl-1,2,3-triazol-4-yl)carbonylamino]methyl]-$l^{3}-oxidanyl-oxidanyl-boron
  • Ligand: water

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Supramolecule #1: 20S immunoproteasome

SupramoleculeName: 20S immunoproteasome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9, #11-#14
Source (natural)Organism: Canis lupus familiaris (dog)

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Macromolecule #1: Proteasome subunit beta

MacromoleculeName: Proteasome subunit beta / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Canis lupus familiaris (dog)
Molecular weightTheoretical: 21.134789 KDa
SequenceString: TIMAVEFDGG VVVGSDSRVS AGEAVVNRAF NKLSPLHQHI YCALSGSAAD AQAMADMAAY QLELHGLELE EPPLVLAAAN VVRNISYKY REDLSAHLMI AGWDRRDGGQ VYGTMGGMLT RQPFAIGGSG STYIYGYVDA AYKPGMSPEE CRSFTTNAIA L AMNRDGSS ...String:
TIMAVEFDGG VVVGSDSRVS AGEAVVNRAF NKLSPLHQHI YCALSGSAAD AQAMADMAAY QLELHGLELE EPPLVLAAAN VVRNISYKY REDLSAHLMI AGWDRRDGGQ VYGTMGGMLT RQPFAIGGSG STYIYGYVDA AYKPGMSPEE CRSFTTNAIA L AMNRDGSS GGVIHLVTIT AAGVDYQVIL GNELPKFYDE

UniProtKB: Proteasome subunit beta

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Macromolecule #2: Proteasome subunit alpha type

MacromoleculeName: Proteasome subunit alpha type / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Canis lupus familiaris (dog)
Molecular weightTheoretical: 29.523564 KDa
SequenceString: MFRNQYDNDV TVWSPQGRIH QIEYAMEAVK QGSATVGLKS KTHAVLVALK RAQSELAAHQ KKILHVDNHI GISIAGLTAD ARLLCNFMR QECLDSRFVF DRPLPVSRLV SLIGSKTQIP TQRYGRRPYG VGLLIAGYDD MGPHIFQTCP SANYFDCRAM S IGARSQSA ...String:
MFRNQYDNDV TVWSPQGRIH QIEYAMEAVK QGSATVGLKS KTHAVLVALK RAQSELAAHQ KKILHVDNHI GISIAGLTAD ARLLCNFMR QECLDSRFVF DRPLPVSRLV SLIGSKTQIP TQRYGRRPYG VGLLIAGYDD MGPHIFQTCP SANYFDCRAM S IGARSQSA RTYLERHMSG FMECNLNELV KHGLRALRET LPAEQDLTTK NVSIGIVGKD LEFTIYDDDD VSPFLEGLEE RP QRKAQPA QPADEPAEKA DEPMEH

UniProtKB: Proteasome subunit alpha type

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Macromolecule #3: Proteasome subunit alpha type

MacromoleculeName: Proteasome subunit alpha type / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Canis lupus familiaris (dog)
Molecular weightTheoretical: 26.435977 KDa
SequenceString: MFLTRSEYDR GVNTFSPEGR LFQVEYAIEA IKLGSTAIGI QTSEGVCLAV EKRITSPLME PSSIEKIVEI DAHIGCAMSG LIADAKTLI DKARVETQNH WFTYNETMTV ESVTQAVSNL ALQFGEEDAD PGAMSRPFGV ALLFGGVDEK GPQLFHMDPS G TFVQCDAR ...String:
MFLTRSEYDR GVNTFSPEGR LFQVEYAIEA IKLGSTAIGI QTSEGVCLAV EKRITSPLME PSSIEKIVEI DAHIGCAMSG LIADAKTLI DKARVETQNH WFTYNETMTV ESVTQAVSNL ALQFGEEDAD PGAMSRPFGV ALLFGGVDEK GPQLFHMDPS G TFVQCDAR AIGSASEGAQ SSLQEVYHKS MTLKEAIKSS LIILKQVMEE KLNATNIELA TVQPGQNFHM FTKEELEEVI KD I

UniProtKB: Proteasome subunit alpha type

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Macromolecule #4: Proteasome subunit alpha type

MacromoleculeName: Proteasome subunit alpha type / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Canis lupus familiaris (dog)
Molecular weightTheoretical: 27.911912 KDa
SequenceString: MSYDRAITVF SPDGHLFQVE YAQEAVKKGS TAVGVRGKDI VVLGVEKKSV AKLQDERTVR KICALDDNVC MAFAGLTADA RIVINRARV ECQSHRLTVE DPVTVEYITR YIASLKQRYT QSNGRRPFGI SALIVGFDFD GTPRLYQTDP SGTYHAWKAN A IGRGAKSV ...String:
MSYDRAITVF SPDGHLFQVE YAQEAVKKGS TAVGVRGKDI VVLGVEKKSV AKLQDERTVR KICALDDNVC MAFAGLTADA RIVINRARV ECQSHRLTVE DPVTVEYITR YIASLKQRYT QSNGRRPFGI SALIVGFDFD GTPRLYQTDP SGTYHAWKAN A IGRGAKSV REFLEKNYTD EAIETDDLTI KLVIKALLEV VQSGGKNIEL AVMRRDQPLK ILNPEEIEKY VAEIEKEKEE NE KKKQKKA S

UniProtKB: Proteasome subunit alpha type

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Macromolecule #5: Proteasome subunit alpha type

MacromoleculeName: Proteasome subunit alpha type / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Canis lupus familiaris (dog)
Molecular weightTheoretical: 29.524791 KDa
SequenceString: MSRRYDSRTT IFSPEGRLYQ VEYAMEAIGH AGTCLGILAN DGVLLAAERR NIHKLLDEVF FSEKIYKLNE DMACSVAGIT SDANVLTNE LRLIAQRYLL QYQEPIPCEQ LVTALCDIKQ AYTQFGGKRP FGVSLLYIGW DKHYGFQLYQ SDPSGNYGGW K ATCIGNNS ...String:
MSRRYDSRTT IFSPEGRLYQ VEYAMEAIGH AGTCLGILAN DGVLLAAERR NIHKLLDEVF FSEKIYKLNE DMACSVAGIT SDANVLTNE LRLIAQRYLL QYQEPIPCEQ LVTALCDIKQ AYTQFGGKRP FGVSLLYIGW DKHYGFQLYQ SDPSGNYGGW K ATCIGNNS AAAVSMLKQD YKEGEMTLKS ALALAIKVLN KTMDVSKLSA EKVEIATLTR ENGKTVIRVL KQKEVEQLIK NH EEEEAKA EREKKEKEQK EKEK

UniProtKB: Proteasome subunit alpha type

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Macromolecule #6: Proteasome subunit alpha type

MacromoleculeName: Proteasome subunit alpha type / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Canis lupus familiaris (dog)
Molecular weightTheoretical: 27.418434 KDa
SequenceString: MSRGSSAGFD RHITIFSPEG RLYQVEYAFK AINQGGLTSV AVRGKDCAVI VTQKKVPDKL LDSSTVTHLF KITENIGCVM TGMTADSRS QVQRARYEAA NWKYKYGYEI PVDMLCKRIA DISQVYTQNA EMRPLGCCMI LIGIDEEQGP QVYKCDPAGY Y CGFKATAA ...String:
MSRGSSAGFD RHITIFSPEG RLYQVEYAFK AINQGGLTSV AVRGKDCAVI VTQKKVPDKL LDSSTVTHLF KITENIGCVM TGMTADSRS QVQRARYEAA NWKYKYGYEI PVDMLCKRIA DISQVYTQNA EMRPLGCCMI LIGIDEEQGP QVYKCDPAGY Y CGFKATAA GVKQTESTSF LEKKVKKKFD WTFEQTVETA ITCLSTVLSI DFKPSEIEVG VVTVENPKFR ILSEAEIDAH LV ALAERD

UniProtKB: Proteasome subunit alpha type

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Macromolecule #7: Proteasome subunit beta

MacromoleculeName: Proteasome subunit beta / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Canis lupus familiaris (dog)
Molecular weightTheoretical: 22.808186 KDa
SequenceString: MEYLIGIQGP DYVLVASDQV AASSIVQMKD DHDKMFKMSE KILLLCVGEA GDTVQFAEYI QKNVQLYKMR NGYELSPTAA ANFTRRNLA DCLRSRTPYH VNLLLAGYDE HEGPALYYMD YLAALAKAPF AAHGYGAFLT LSILDRYYTP TISRERAVEL L RKCLEELQ ...String:
MEYLIGIQGP DYVLVASDQV AASSIVQMKD DHDKMFKMSE KILLLCVGEA GDTVQFAEYI QKNVQLYKMR NGYELSPTAA ANFTRRNLA DCLRSRTPYH VNLLLAGYDE HEGPALYYMD YLAALAKAPF AAHGYGAFLT LSILDRYYTP TISRERAVEL L RKCLEELQ KRFILNLPTF SVRIIDKNGI HDLDNISFPK QGS

UniProtKB: Proteasome subunit beta

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Macromolecule #8: Proteasome subunit beta

MacromoleculeName: Proteasome subunit beta / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Canis lupus familiaris (dog)
Molecular weightTheoretical: 23.002922 KDa
SequenceString: MSIMSYNGGA VMAMKGKNCV AIAADRRFGI QAQMVTTDFQ KIFPMGDRLY IGLAGLATDV QTVAQRLKFR LNLYELKEGR QIKPYTLMS MVANLLYEKR FGPYYTEPVI AGLDPKTFKP FICSLDLIGC PMVTDDFVVS GTCSEQMYGM CESLWEPNMD P EHLFETIS ...String:
MSIMSYNGGA VMAMKGKNCV AIAADRRFGI QAQMVTTDFQ KIFPMGDRLY IGLAGLATDV QTVAQRLKFR LNLYELKEGR QIKPYTLMS MVANLLYEKR FGPYYTEPVI AGLDPKTFKP FICSLDLIGC PMVTDDFVVS GTCSEQMYGM CESLWEPNMD P EHLFETIS QAMLNAVDRD AVSGMGVIVH IIEKDKITTR TLKARMD

UniProtKB: Proteasome subunit beta

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Macromolecule #9: Proteasome subunit beta

MacromoleculeName: Proteasome subunit beta / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Canis lupus familiaris (dog)
Molecular weightTheoretical: 29.191088 KDa
SequenceString: MEAFLESRSR VWAGGPAPGQ FYHIPPSSVA SVEPAFSPYG GPVTRTQNPM VTGTSVLGVK FEGGVVIAAD MLGSYGSLAR FRNISRIMR VNDSTMLGAS GDYADFQYLK QVLGQMVIDE ELLGDGHSYS PRAIHSWLTR AMYSRRSKMN PLWNTMVIGG Y ADGESFLG ...String:
MEAFLESRSR VWAGGPAPGQ FYHIPPSSVA SVEPAFSPYG GPVTRTQNPM VTGTSVLGVK FEGGVVIAAD MLGSYGSLAR FRNISRIMR VNDSTMLGAS GDYADFQYLK QVLGQMVIDE ELLGDGHSYS PRAIHSWLTR AMYSRRSKMN PLWNTMVIGG Y ADGESFLG YVDMLGVAYE APSLATGYGA YLAQPLLREV LEKQPVLSQT EARELVERCM RVLYYRDARS YNRFQIATVT EK GVEIEGP LSAETNWEIA HMISGFE

UniProtKB: Proteasome subunit beta

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Macromolecule #10: Proteasome subunit beta type-8

MacromoleculeName: Proteasome subunit beta type-8 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Canis lupus familiaris (dog)
Molecular weightTheoretical: 22.629408 KDa
SequenceString: TTLAFKFQHG VIVAVDSRAT AGNYISSSRV NKVIEINPSL LGTMSGCAAD CQYWERLLAK ECRLYYLRNG ERISVSAASK LLSNMVYQY RGMDLSMGSM ICGWDKKGPG LYYVDQNGTR LSGNMFSTGS GSTYAYGVMD SGYQPSLSPE EAYELGRRAI T YATHRDSY ...String:
TTLAFKFQHG VIVAVDSRAT AGNYISSSRV NKVIEINPSL LGTMSGCAAD CQYWERLLAK ECRLYYLRNG ERISVSAASK LLSNMVYQY RGMDLSMGSM ICGWDKKGPG LYYVDQNGTR LSGNMFSTGS GSTYAYGVMD SGYQPSLSPE EAYELGRRAI T YATHRDSY SGGIINMYHM KEDGWVKVES TDVNELLHQY QEANQ

UniProtKB: Proteasome subunit beta type-8

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Macromolecule #11: Proteasome subunit alpha type

MacromoleculeName: Proteasome subunit alpha type / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Canis lupus familiaris (dog)
Molecular weightTheoretical: 25.927535 KDa
SequenceString: MAERGYSFSL TTFSPSGKLV QIEYALAAVA GGAPSVGIKA ANGVVLATEK KQKSILYDER SVHKVEPITK HIGLVYSGMG PDYRVLVHR ARKLAQQYYL VYQEPIPTAQ LVQRVASVMQ EYTQSGGVRP FGVSLLICGW NEGRPYLFQS DPSGAYFAWK A TAMGKNYV ...String:
MAERGYSFSL TTFSPSGKLV QIEYALAAVA GGAPSVGIKA ANGVVLATEK KQKSILYDER SVHKVEPITK HIGLVYSGMG PDYRVLVHR ARKLAQQYYL VYQEPIPTAQ LVQRVASVMQ EYTQSGGVRP FGVSLLICGW NEGRPYLFQS DPSGAYFAWK A TAMGKNYV NGKTFLEKRY NEDLELEDAI HTAILTLKES FEGQMTEDNI EVGICNEAGF RRLTPTEVKD YLAAIA

UniProtKB: Proteasome subunit alpha type

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Macromolecule #12: Proteasome subunit beta

MacromoleculeName: Proteasome subunit beta / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Canis lupus familiaris (dog)
Molecular weightTheoretical: 26.431156 KDa
SequenceString: MLSTAARGWG PGRDLAMEPD GAAGPQQLRF SPYAFNGGTV LAIAGEDFSI VASDTRLSEG FSIHTRDSPK CYKLTDKTVI GCSGFHGDC LTLTKIIEAR LKMYKHSNNK TMTTGAIAAM LSTILYSRRF FPYYVYNIIG GLDEEGKGAV YSFDPVGSYQ R DSFKAGGS ...String:
MLSTAARGWG PGRDLAMEPD GAAGPQQLRF SPYAFNGGTV LAIAGEDFSI VASDTRLSEG FSIHTRDSPK CYKLTDKTVI GCSGFHGDC LTLTKIIEAR LKMYKHSNNK TMTTGAIAAM LSTILYSRRF FPYYVYNIIG GLDEEGKGAV YSFDPVGSYQ R DSFKAGGS ASAMLQPLLD NQVGFKNMQN VEHVPLSLDR AMRLVKDVFI SAAERDVYTG DALRICIVTK EGIREETVPL RK D

UniProtKB: Proteasome subunit beta

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Macromolecule #13: Proteasome subunit alpha type

MacromoleculeName: Proteasome subunit alpha type / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Canis lupus familiaris (dog)
Molecular weightTheoretical: 28.484326 KDa
SequenceString: MSSIGTGYDL SASTFSPDGR VFQVEYAMKA VENSSTAIGI RCKDGVVFGV EKLVLSKLYE EGSNKRLFNV DRHVGMAVAG LLADARSLA DIAREEASNF RSNFGYNIPL KHLADRVAMY VHAYTLYSAV RPFGCSFMLG SYSVNDGAQL YMIDPSGVSY G YWGCAIGK ...String:
MSSIGTGYDL SASTFSPDGR VFQVEYAMKA VENSSTAIGI RCKDGVVFGV EKLVLSKLYE EGSNKRLFNV DRHVGMAVAG LLADARSLA DIAREEASNF RSNFGYNIPL KHLADRVAMY VHAYTLYSAV RPFGCSFMLG SYSVNDGAQL YMIDPSGVSY G YWGCAIGK ARQAAKTEIE KLQMKEMTCR DIVKEVAKII YIVHDEVKDK AFELELSWVG EITKGRHEIV PKDIREEAEK YA KESLKEE DESDDDNM

UniProtKB: Proteasome subunit alpha type

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Macromolecule #14: Proteasome subunit beta

MacromoleculeName: Proteasome subunit beta / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Canis lupus familiaris (dog)
Molecular weightTheoretical: 24.884293 KDa
SequenceString: TTIAGLVFRD GVILGADTRA TNDSVVMDKN CEKIHFIAPK IYCCGAGVAA DAEMTTRMAA SNMELHSLST GREPRVTTVT RLLRQTLFR YRGHVGASLL VGGVDFSGPQ LYSVHPHGSY SRLPFTALGS GQDAALAVLE DRFQPNMTLE AAQELLVEAI T AGILGDLG ...String:
TTIAGLVFRD GVILGADTRA TNDSVVMDKN CEKIHFIAPK IYCCGAGVAA DAEMTTRMAA SNMELHSLST GREPRVTTVT RLLRQTLFR YRGHVGASLL VGGVDFSGPQ LYSVHPHGSY SRLPFTALGS GQDAALAVLE DRFQPNMTLE AAQELLVEAI T AGILGDLG SGGSVDACVI TGTGAKLLRT LSSPTKPTER PSQYYFAPGT TAVQSQTVKP LTLELLEETV QAMEVE

UniProtKB: Proteasome subunit beta

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Macromolecule #15: [(2~{R},3~{R})-3-azanyl-4-oxidanyl-butan-2-yl]oxy-[(~{R})-cyclohe...

MacromoleculeName: [(2~{R},3~{R})-3-azanyl-4-oxidanyl-butan-2-yl]oxy-[(~{R})-cyclohexyl-[(1-cyclohexyl-1,2,3-triazol-4-yl)carbonylamino]methyl]-$l^{3}-oxidanyl-oxidanyl-boron
type: ligand / ID: 15 / Number of copies: 4 / Formula: A1L0D
Molecular weightTheoretical: 439.357 Da

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Macromolecule #16: water

MacromoleculeName: water / type: ligand / ID: 16 / Number of copies: 16 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 56.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 304965
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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