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- EMDB-10586: Rat 20S proteasome -

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Basic information

Entry
Database: EMDB / ID: EMD-10586
TitleRat 20S proteasome
Map dataendogenous rat liver 20S proteasome, local resolution filtered
Sample
  • Complex: Rat liver 20S proteasome
    • Protein or peptide: x 14 types
Function / homology
Function and homology information


Cross-presentation of soluble exogenous antigens (endosomes) / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of ornithine decarboxylase (ODC) / Assembly of the pre-replicative complex / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / 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 ...Cross-presentation of soluble exogenous antigens (endosomes) / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of ornithine decarboxylase (ODC) / Assembly of the pre-replicative complex / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / 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 / Autodegradation of the E3 ubiquitin ligase COP1 / Asymmetric localization of PCP proteins / Degradation of DVL / Hedgehog ligand biogenesis / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of GLI1 by the proteasome / Hedgehog 'on' state / TNFR2 non-canonical NF-kB pathway / NIK-->noncanonical NF-kB signaling / UCH proteinases / 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 / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Regulation of RUNX3 expression and activity / GLI3 is processed to GLI3R by the proteasome / Activation of NF-kappaB in B cells / Degradation of beta-catenin by the destruction complex / Degradation of AXIN / Regulation of RAS by GAPs / Orc1 removal from chromatin / Neddylation / AUF1 (hnRNP D0) binds and destabilizes mRNA / MAPK6/MAPK4 signaling / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / Separation of Sister Chromatids / Antigen processing: Ubiquitination & Proteasome degradation / ABC-family proteins mediated transport / Ub-specific processing proteases / : / proteasome core complex / Neutrophil degranulation / immune system process / myofibril / NF-kappaB binding / 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 / response to organonitrogen compound / proteasome complex / proteolysis involved in protein catabolic process / sarcomere / ciliary basal body / proteasomal protein catabolic process / P-body / lipopolysaccharide binding / response to virus / response to organic cyclic compound / nuclear matrix / positive regulation of NF-kappaB transcription factor activity / peptidase activity / ubiquitin-dependent protein catabolic process / postsynapse / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / response to oxidative stress / ribosome / centrosome / synapse / ubiquitin protein ligase binding / proteolysis / RNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
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 alpha type-2 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-4 / Proteasome subunit beta type-6 / Proteasome subunit beta type-5 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-4 / Proteasome subunit beta type-3 ...Proteasome subunit alpha type-2 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-4 / Proteasome subunit beta type-6 / Proteasome subunit beta type-5 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-4 / Proteasome subunit beta type-3 / Proteasome subunit beta type-2 / Proteasome subunit alpha type-7 / Proteasome subunit alpha type-6 / Proteasome subunit beta type-7
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat) / Norway rat (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsDeshmukh FK / Polkinghorn CR / Elad N / Sharon M
Funding support Israel, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)636752 Israel
Israel Science Foundation300/17 Israel
CitationJournal: ACS Cent Sci / Year: 2020
Title: Comparative Structural Analysis of 20S Proteasome Ortholog Protein Complexes by Native Mass Spectrometry.
Authors: Shay Vimer / Gili Ben-Nissan / David Morgenstern / Fanindra Kumar-Deshmukh / Caley Polkinghorn / Royston S Quintyn / Yury V Vasil'ev / Joseph S Beckman / Nadav Elad / Vicki H Wysocki / Michal Sharon /
Abstract: Ortholog protein complexes are responsible for equivalent functions in different organisms. However, during evolution, each organism adapts to meet its physiological needs and the environmental ...Ortholog protein complexes are responsible for equivalent functions in different organisms. However, during evolution, each organism adapts to meet its physiological needs and the environmental challenges imposed by its niche. This selection pressure leads to structural diversity in protein complexes, which are often difficult to specify, especially in the absence of high-resolution structures. Here, we describe a multilevel experimental approach based on native mass spectrometry (MS) tools for elucidating the structural preservation and variations among highly related protein complexes. The 20S proteasome, an essential protein degradation machinery, served as our model system, wherein we examined five complexes isolated from different organisms. We show that throughout evolution, from the archaeal prokaryotic complex to the eukaryotic 20S proteasomes in yeast () and mammals (rat - , rabbit - and human - HEK293 cells), the proteasome increased both in size and stability. Native MS structural signatures of the rat and rabbit 20S proteasomes, which heretofore lacked high-resolution, three-dimensional structures, highly resembled that of the human complex. Using cryoelectron microscopy single-particle analysis, we were able to obtain a high-resolution structure of the rat 20S proteasome, allowing us to validate the MS-based results. Our study also revealed that the yeast complex, and not those in mammals, was the largest in size and displayed the greatest degree of kinetic stability. Moreover, we also identified a new proteoform of the PSMA7 subunit that resides within the rat and rabbit complexes, which to our knowledge have not been previously described. Altogether, our strategy enables elucidation of the unique structural properties of protein complexes that are highly similar to one another, a framework that is valid not only to ortholog protein complexes, but also for other highly related protein assemblies.
History
DepositionJan 2, 2020-
Header (metadata) releaseMay 13, 2020-
Map releaseMay 13, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.043
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.043
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6tu3
  • Surface level: 0.043
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10586.png

Downloads & links

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Map

FileDownload / File: emd_10586.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationendogenous rat liver 20S proteasome, local resolution filtered
Voxel sizeX=Y=Z: 0.86 Å
Density
Contour LevelBy AUTHOR: 0.043 / Movie #1: 0.043
Minimum - Maximum-0.16117156 - 0.2472638
Average (Standard dev.)-0.000010448684 (±0.006311661)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 344.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.860.860.86
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z344.000344.000344.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.1610.247-0.000

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Supplemental data

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Mask #1

Fileemd_10586_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Rat 20S proteasome, Unfiltered half map 2

Fileemd_10586_half_map_1.map
AnnotationRat 20S proteasome, Unfiltered half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Rat 20S proteasome, Unfiltered half map 1

Fileemd_10586_half_map_2.map
AnnotationRat 20S proteasome, Unfiltered half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Rat liver 20S proteasome

EntireName: Rat liver 20S proteasome
Components
  • Complex: Rat liver 20S proteasome
    • Protein or peptide: Proteasome subunit alpha type-6
    • Protein or peptide: Proteasome subunit alpha type-2
    • Protein or peptide: Proteasome subunit alpha type-4
    • Protein or peptide: Proteasome subunit alpha type-7
    • Protein or peptide: Proteasome subunit alpha type-5
    • Protein or peptide: Proteasome subunit alpha type-1
    • Protein or peptide: Proteasome subunit alpha type-3
    • Protein or peptide: Proteasome subunit beta type-6
    • Protein or peptide: Proteasome subunit beta type-7
    • Protein or peptide: Proteasome subunit beta type-3PSMB3
    • Protein or peptide: Proteasome subunit beta type-2PSMB2
    • Protein or peptide: Proteasome subunit beta type-5PSMB5
    • Protein or peptide: Proteasome subunit beta type-1PSMB1
    • Protein or peptide: Proteasome subunit beta type-4PSMB4

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Supramolecule #1: Rat liver 20S proteasome

SupramoleculeName: Rat liver 20S proteasome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Endogenous 20S proteasome purified from the rat livers by anion-exchange chromatography
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: Proteasome subunit alpha type-6

MacromoleculeName: Proteasome subunit alpha type-6 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Norway rat (Norway rat)
Molecular weightTheoretical: 27.432459 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 ILTEAEIDAH LV ALAERD

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Macromolecule #2: Proteasome subunit alpha type-2

MacromoleculeName: Proteasome subunit alpha type-2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Norway rat (Norway rat)
Molecular weightTheoretical: 25.955549 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 RRLTPTEVRD YLAAIA

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Macromolecule #3: Proteasome subunit alpha type-4

MacromoleculeName: Proteasome subunit alpha type-4 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Norway rat (Norway rat)
Molecular weightTheoretical: 29.53983 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 ALALAVKVLN KTMDVSKLSA EKVEIATLTR ENGKTVIRVL KQKEVEQLIK KH EEEEAKA EREKKEKEQR EKDK

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Macromolecule #4: Proteasome subunit alpha type-7

MacromoleculeName: Proteasome subunit alpha type-7 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Norway rat (Norway rat)
Molecular weightTheoretical: 28.369439 KDa
SequenceString: MSYDRAITVF SPDGHLFQVE YAQEAVKKGS TAVGVRGRDI VVLGVEKKSV AKLQDERTVR KICALDDNVC MAFAVVASVS GLTADARIV INRARVECQS HRLTVGDPVT VEYITRYIAS LKQRYTQSNG RRPFGISALI VGFDFDGTPR LYQTDPSGTY H AWKANAIG ...String:
MSYDRAITVF SPDGHLFQVE YAQEAVKKGS TAVGVRGRDI VVLGVEKKSV AKLQDERTVR KICALDDNVC MAFAVVASVS GLTADARIV INRARVECQS HRLTVGDPVT VEYITRYIAS LKQRYTQSNG RRPFGISALI VGFDFDGTPR LYQTDPSGTY H AWKANAIG RGAKSVREFL EKNYTDDAIE TDDLTIKLVI KALLEVVQSG GKNIELAVMR RDQPLKILSP EEIEKYVAEI EK EKEENEK KKQKKAS

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Macromolecule #5: Proteasome subunit alpha type-5

MacromoleculeName: Proteasome subunit alpha type-5 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Norway rat (Norway rat)
Molecular weightTheoretical: 26.41685 KDa
SequenceString: MFLTRSEYDR GVNTFSPEGR LFQVEYAIEG HKLGSTAIGI QTSEGVCLAV EKRITSPLME PSSIEKIVEI DAHIGCAMSG LIADAKTLI DKARVETQNH WFTYNETMTV ESVTQAVSNL ALQFGEEDAD PGAMSRPFGV ALLFGGVDEK GPQLFHMDPS G TFVQCDAR ...String:
MFLTRSEYDR GVNTFSPEGR LFQVEYAIEG HKLGSTAIGI QTSEGVCLAV EKRITSPLME PSSIEKIVEI DAHIGCAMSG LIADAKTLI DKARVETQNH WFTYNETMTV ESVTQAVSNL ALQFGEEDAD PGAMSRPFGV ALLFGGVDEK GPQLFHMDPS G TFVQCDAR AIGSASEGAQ SSLQEVYHKS TTLKEAIKSS LIILKQVMEE KLNATNIELA TVQPGQNFHM FTKEELEEVI KD I

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Macromolecule #6: Proteasome subunit alpha type-1

MacromoleculeName: Proteasome subunit alpha type-1 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Norway rat (Norway rat)
Molecular weightTheoretical: 29.557541 KDa
SequenceString: MFRNQYDNDV TVWSPQGRIH QIEYAMEAVK QGSATVGLKS KTHAVLVALK RAQSELAAHQ KKILHVDNHI GISIAGLTAD ARLLCNFMR QECLDSRFVF DRPLPVSRLV SLIGSKTQIP TQRYGRRPYG VGLLIAGYDD MGPHVFQTCP SANYFDCRAM S IGARSQSA ...String:
MFRNQYDNDV TVWSPQGRIH QIEYAMEAVK QGSATVGLKS KTHAVLVALK RAQSELAAHQ KKILHVDNHI GISIAGLTAD ARLLCNFMR QECLDSRFVF DRPLPVSRLV SLIGSKTQIP TQRYGRRPYG VGLLIAGYDD MGPHVFQTCP SANYFDCRAM S IGARSQSA RTYLERHMSE FMQCNLDELV KHGLRALRET LPAEQDLTTK NVSIGIVGKD LEFTIYDDDD VSPFLDGLEE RP QRKAQPS QAADEPAEKA DEPMEH

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Macromolecule #7: Proteasome subunit alpha type-3

MacromoleculeName: Proteasome subunit alpha type-3 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Norway rat (Norway rat)
Molecular weightTheoretical: 28.456275 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 DVVKEVAKII YIVHDEVKDK AFELELSWVG ELTKGRHEIV PKDVREEAEK YA KESLKEE DESDDDNM

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Macromolecule #8: Proteasome subunit beta type-6

MacromoleculeName: Proteasome subunit beta type-6 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Norway rat (Norway rat)
Molecular weightTheoretical: 25.309576 KDa
SequenceString: MAAALAVRGA VSAPAFGPEA LTPDWENREV STGTTIMAVQ FDGGVVLGAD SRTTTGSYIA NRVTDKLTPI HDHIFCCRSG SAADTQAVA DAVTYQLGFH SIELNEPPLV HTAASLFKEM CYRYREDLMA GIIIAGWDPQ EGGQVYSVPM GGMMVRQSFA I GGSGSSYI ...String:
MAAALAVRGA VSAPAFGPEA LTPDWENREV STGTTIMAVQ FDGGVVLGAD SRTTTGSYIA NRVTDKLTPI HDHIFCCRSG SAADTQAVA DAVTYQLGFH SIELNEPPLV HTAASLFKEM CYRYREDLMA GIIIAGWDPQ EGGQVYSVPM GGMMVRQSFA I GGSGSSYI YGYVDATYRE GMTKDECLQF TANALALAME RDGSSGGVIR LAAIQQSGVE RQVLLGDQIP KVTISTLPPP

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Macromolecule #9: Proteasome subunit beta type-7

MacromoleculeName: Proteasome subunit beta type-7 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Norway rat (Norway rat)
Molecular weightTheoretical: 29.963461 KDa
SequenceString: MAAVSVFQAP VGGFSFDNCR RNAVLEADFA KKGFKLPKAR KTGTTIAGVV YKDGIVLGAD TRATEGMVVA DKNCSKIHFI SPNIYCCGA GTAADTDMTT QLISSNLELH SLTTGRLPRV VTANRMLKQM LFRYQGYIGA ALVLGGVDVT GPHLYSIYPH G STDKLPYV ...String:
MAAVSVFQAP VGGFSFDNCR RNAVLEADFA KKGFKLPKAR KTGTTIAGVV YKDGIVLGAD TRATEGMVVA DKNCSKIHFI SPNIYCCGA GTAADTDMTT QLISSNLELH SLTTGRLPRV VTANRMLKQM LFRYQGYIGA ALVLGGVDVT GPHLYSIYPH G STDKLPYV TMGSGSLAAM AVFEDKFRPD MEEEEAKKLV SEAIAAGIFN DLGSGSNIDL CVISKSKLDF LRPYSVPNKK GT RFGRYRC EKGTTAVLTE KVTPLELEVL EEIVQTMDTS

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Macromolecule #10: Proteasome subunit beta type-3

MacromoleculeName: Proteasome subunit beta type-3 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Norway rat (Norway rat)
Molecular weightTheoretical: 22.988895 KDa
SequenceString: MSVMSYNGGA VMAMKGKNCV AIAADRRFGI QAQMVTTDFQ KIFPMGDRLY IGLAGLATDV QTVAQRLKFR LNLYELKEGR QIKPYTLMS MVANLLYEKR FGPYYTEPVI AGLDPKTFKP FICSLDLIGC PMVTDDFVVS GTCSEQMYGM CESLWEPNMD P EHLFETIS ...String:
MSVMSYNGGA VMAMKGKNCV AIAADRRFGI QAQMVTTDFQ KIFPMGDRLY IGLAGLATDV QTVAQRLKFR LNLYELKEGR QIKPYTLMS MVANLLYEKR FGPYYTEPVI AGLDPKTFKP FICSLDLIGC PMVTDDFVVS GTCSEQMYGM CESLWEPNMD P EHLFETIS QAMLNAVDRD AVSGMGVIVH IIEKDKITTR TLKARMD

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Macromolecule #11: Proteasome subunit beta type-2

MacromoleculeName: Proteasome subunit beta type-2 / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Norway rat (Norway rat)
Molecular weightTheoretical: 22.941381 KDa
SequenceString: MEYLIGIQGP DYVLVASDRV AASNIVQMKD DHDKMFKMSE KILLLCVGEA GDTVQFAEYI QKNVQLYKMR NGYELSPTAA ANFTRRNLA DCLRSRTPYH VNLLLAGYDE HEGPALYYMD YLAALAKAPF AAHGYGAFLT LSILDRYYTP TISRERAVEL L RKCLEELQ ...String:
MEYLIGIQGP DYVLVASDRV AASNIVQMKD DHDKMFKMSE KILLLCVGEA GDTVQFAEYI QKNVQLYKMR NGYELSPTAA ANFTRRNLA DCLRSRTPYH VNLLLAGYDE HEGPALYYMD YLAALAKAPF AAHGYGAFLT LSILDRYYTP TISRERAVEL L RKCLEELQ KRFILNLPTF SVRVIDKDGI HNLENITFTK RSS

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Macromolecule #12: Proteasome subunit beta type-5

MacromoleculeName: Proteasome subunit beta type-5 / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Norway rat (Norway rat)
Molecular weightTheoretical: 28.615408 KDa
SequenceString: MALASVLQRP MPVNQHGFFG LGGRADLLDL GPGSPGDGLS LAAPSWGVPE EPRIEMLHGT TTLAFKFQHG VIVAADSRAT AGPYIASQT VKKVIEINPY LLGTMAGGAA DCSFWERLLA RQCRIYELRN KERISVAAAS KLLANMVYQY KGMGLSMGTM I CGWDKRGP ...String:
MALASVLQRP MPVNQHGFFG LGGRADLLDL GPGSPGDGLS LAAPSWGVPE EPRIEMLHGT TTLAFKFQHG VIVAADSRAT AGPYIASQT VKKVIEINPY LLGTMAGGAA DCSFWERLLA RQCRIYELRN KERISVAAAS KLLANMVYQY KGMGLSMGTM I CGWDKRGP GLYYVDSEGN RISGTAFSVG SGSVYAFGVM DRGYSYDLQV EEAYDLARRA IYQATYRDAY SGGAVNLYHV RE DGWIRVS SDNVADLHDK YTSSIP

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Macromolecule #13: Proteasome subunit beta type-1

MacromoleculeName: Proteasome subunit beta type-1 / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Norway rat (Norway rat)
Molecular weightTheoretical: 26.511301 KDa
SequenceString: MLSTAAYRDP DRELVMGPQG SAGPVQMRFS PYAFNGGTVL AIAGEDFSIV ASDTRLSEGF SIHTRDSPKC YKLTDKTVIG CSGFHGDCL TLTKIIEARL KMYKHSNNKA MTTGAIAAML STILYSRRFF PYYVYNIIEG LDEEGKGAVY SFDPVGSYQR D SFKAGGSA ...String:
MLSTAAYRDP DRELVMGPQG SAGPVQMRFS PYAFNGGTVL AIAGEDFSIV ASDTRLSEGF SIHTRDSPKC YKLTDKTVIG CSGFHGDCL TLTKIIEARL KMYKHSNNKA MTTGAIAAML STILYSRRFF PYYVYNIIEG LDEEGKGAVY SFDPVGSYQR D SFKAGGSA SAMLQPLLDN QVGFKNMQNV EHVPLTLDRA MRLVKDVFIS AAERDVYTGD ALRICIVTKE GIREETVPLR KD

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Macromolecule #14: Proteasome subunit beta type-4

MacromoleculeName: Proteasome subunit beta type-4 / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Norway rat (Norway rat)
Molecular weightTheoretical: 29.226248 KDa
SequenceString: MEAFWESRTG HWAGGPAPGQ FYRVPSTPSC LMDPMSAPAR PITRTQNPMV TGTSVLGVKF DCGVVIAADM LGSYGSLARF RNISRIMRV NDSTMLGASG DYADFQYLKQ VLGQMVIDEE LFGDGHSYSP RAIHSWLTRA MYSRRSKMNP LWNTKVIGGY A GGESFLGY ...String:
MEAFWESRTG HWAGGPAPGQ FYRVPSTPSC LMDPMSAPAR PITRTQNPMV TGTSVLGVKF DCGVVIAADM LGSYGSLARF RNISRIMRV NDSTMLGASG DYADFQYLKQ VLGQMVIDEE LFGDGHSYSP RAIHSWLTRA MYSRRSKMNP LWNTKVIGGY A GGESFLGY VDMLGVAYEA PSLATGYGAY LAQPLLREVL EKQPVLSQTE ARELVERCMR VLYYRDARSY NRFQVATVTE KG VEIEGPL SAQTNWDIAH MISGFE

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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

Concentration14 mg/mL
BufferpH: 7.4 / Component - Concentration: 160.0 mM / Component - Formula: K3PO4 / Component - Name: Potassium phosphate
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.052 kPa
Details: Grids were glow discharged 30 minutes before applying the sample.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 3 seconds.
DetailsPurified endogenous rat liver 20S proteasome

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: DIFFRACTION / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
DetailsPreliminary grid screening was performed on Talos Arctica
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 2234 / Average exposure time: 1.5 sec. / Average electron dose: 37.0 e/Å2
Details: Images were collected in movie-mode at 45 frames per second
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 284161
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6rgq


Details: Recombinant human 20S proteasome
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 245800
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-6tu3:
Rat 20S proteasome

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