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- EMDB-52296: CryoEM structure of human 20S proteasome in complex with proteaso... -

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Basic information

Entry
Database: EMDB / ID: EMD-52296
TitleCryoEM structure of human 20S proteasome in complex with proteasome inhibitor Salinosporamid A
Map dataThis map has been used for building the atomic model. it was obtained by flipping the handedness of the Volume obtained after the final refinement and subsequent sharpening via the EMReady software
Sample
  • Complex: Human 20S proteasome in complex with proteasome inhibitor Salinosporamid A
    • Protein or peptide: x 11 types
  • Protein or peptide: x 3 types
  • Ligand: x 1 types
KeywordsInhibitor / 20S proteasome / Salinosporamid A / HYDROLASE
Function / homology
Function and homology information


purine ribonucleoside triphosphate binding / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / proteasome core complex / Somitogenesis / myofibril / immune system process / NF-kappaB binding / proteasome endopeptidase complex ...purine ribonucleoside triphosphate binding / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / proteasome core complex / Somitogenesis / myofibril / immune system process / NF-kappaB binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome assembly / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteasome complex / proteolysis involved in protein catabolic process / sarcomere / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / lipopolysaccharide binding / Degradation of AXIN / Hh mutants are degraded by ERAD / negative regulation of inflammatory response to antigenic stimulus / P-body / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / G2/M Checkpoints / Defective CFTR causes cystic fibrosis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Negative regulation of NOTCH4 signaling / Vif-mediated degradation of APOBEC3G / Regulation of RUNX3 expression and activity / Hedgehog 'on' state / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / MAPK6/MAPK4 signaling / : / Degradation of beta-catenin by the destruction complex / response to virus / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / ABC-family proteins mediated transport / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / nuclear matrix / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / positive regulation of NF-kappaB transcription factor activity / Regulation of RUNX2 expression and activity / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / UCH proteinases / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / peptidase activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / ER-Phagosome pathway / regulation of inflammatory response / secretory granule lumen / endopeptidase activity / response to oxidative stress / proteasome-mediated ubiquitin-dependent protein catabolic process / ficolin-1-rich granule lumen / Ub-specific processing proteases / nuclear body / ciliary basal body / cilium / ribosome / cadherin binding / intracellular membrane-bounded organelle / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / mitochondrion / proteolysis / RNA binding / extracellular exosome
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 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
Similarity search - Domain/homology
Proteasome subunit alpha type-7 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-4 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-4 / Proteasome subunit beta type-6 / Proteasome subunit beta type-5 ...Proteasome subunit alpha type-7 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-4 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-4 / Proteasome subunit beta type-6 / Proteasome subunit beta type-5 / Proteasome subunit beta type-3 / Proteasome subunit beta type-2 / Proteasome subunit alpha type-6 / Proteasome subunit beta type-7
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsSuelzen H / Boura E / Silhan J
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: bioRxiv / Year: 2025
Title: Structural insights into Salinosporamide A mediated inhibition of the human 20S proteasome.
Authors: Hagen Sülzen / Pavla Fajtova / Anthony J O'Donoghue / Evzen Boura / Jan Silhan /
Abstract: The 20S proteasome, a critical component of the ubiquitin-proteasome system, plays a central role in regulating protein degradation in eukaryotic cells. Marizomib (MZB), a natural γ-lactam-β- ...The 20S proteasome, a critical component of the ubiquitin-proteasome system, plays a central role in regulating protein degradation in eukaryotic cells. Marizomib (MZB), a natural γ-lactam-β-lactone compound derived from , is a potent 20S proteasome covalent inhibitor with demonstrated anticancer properties. Its broad-spectrum inhibition of all three proteasome subunits and ability to cross the blood-brain barrier has made it a promising therapeutic candidate for glioblastoma. Here, we present the cryo-EM structure of the human 20S proteasome in complex with MZB at 2.55 Å resolution. This structure reveals the binding mode of MZB to all six catalytic subunits within the two β-rings of the 20S proteasome, providing a detailed molecular understanding of its irreversible inhibitory mechanism. These findings explain the therapeutic potential of MZB at the molecular level and highlight marine-derived natural products in targeting the proteasome for anticancer treatment.
History
DepositionDec 9, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52296.png

Downloads & links

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Map

FileDownload / File: emd_52296.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis map has been used for building the atomic model. it was obtained by flipping the handedness of the Volume obtained after the final refinement and subsequent sharpening via the EMReady software
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 333.44 Å		0.83 Å/pix.
x 400 pix.
= 333.44 Å		0.83 Å/pix.
x 400 pix.
= 333.44 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8336 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 8.0
Minimum - Maximum-0.5213783 - 28.965886999999999
Average (Standard dev.)0.04976961 (±0.97099334)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 333.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52296_msk_1.map
Projections & Slices
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Additional map: Unsharpened density map obtained in the final refinement...

Fileemd_52296_additional_1.map
AnnotationUnsharpened density map obtained in the final refinement step. Handedness of this reconstruction was flipped using Chimera.
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Handedness of half maps was flipped using Chimera.

Fileemd_52296_half_map_1.map
AnnotationHandedness of half maps was flipped using Chimera.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Handedness of half maps was flipped using Chimera.

Fileemd_52296_half_map_2.map
AnnotationHandedness of half maps was flipped using Chimera.
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram (log scale)

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Sample components

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Entire : Human 20S proteasome in complex with proteasome inhibitor Salinos...

EntireName: Human 20S proteasome in complex with proteasome inhibitor Salinosporamid A
Components
  • Complex: Human 20S proteasome in complex with proteasome inhibitor Salinosporamid A
    • 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-5
    • Protein or peptide: Proteasome subunit alpha type-1
    • Protein or peptide: Proteasome subunit alpha type-3
    • Protein or peptide: Proteasome subunit beta type-3
    • Protein or peptide: Proteasome subunit beta type-2
    • Protein or peptide: Proteasome subunit beta type-1
    • Protein or peptide: Proteasome subunit beta type-4
    • Protein or peptide: Proteasome subunit alpha type-7
  • Protein or peptide: Proteasome subunit beta type-6
  • Protein or peptide: Proteasome subunit beta type-7
  • Protein or peptide: Proteasome subunit beta type-5
  • Ligand: (3AR,6R,6AS)-6-((S)-((S)-CYCLOHEX-2-ENYL)(HYDROXY)METHYL)-6A-METHYL-4-OXO-HEXAHYDRO-2H-FURO[3,2-C]PYRROLE-6-CARBALDEHYDE

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Supramolecule #1: Human 20S proteasome in complex with proteasome inhibitor Salinos...

SupramoleculeName: Human 20S proteasome in complex with proteasome inhibitor Salinosporamid A
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11
Source (natural)Organism: Homo sapiens (human)

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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
Source (natural)Organism: Homo sapiens (human)
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

UniProtKB: Proteasome subunit alpha type-6

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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
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.796338 KDa
SequenceString: AERGYSFSLT TFSPSGKLVQ IEYALAAVAG GAPSVGIKAA NGVVLATEKK QKSILYDERS VHKVEPITKH IGLVYSGMGP DYRVLVHRA RKLAQQYYLV YQEPIPTAQL VQRVASVMQE YTQSGGVRPF GVSLLICGWN EGRPYLFQSD PSGAYFAWKA T AMGKNYVN ...String:
AERGYSFSLT TFSPSGKLVQ IEYALAAVAG GAPSVGIKAA NGVVLATEKK QKSILYDERS VHKVEPITKH IGLVYSGMGP DYRVLVHRA RKLAQQYYLV YQEPIPTAQL VQRVASVMQE YTQSGGVRPF GVSLLICGWN EGRPYLFQSD PSGAYFAWKA T AMGKNYVN GKTFLEKRYN EDLELEDAIH TAILTLKESF EGQMTEDNIE VGICNEAGFR RLTPTEVKDY LAAIA

UniProtKB: Proteasome subunit alpha type-2

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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: Homo sapiens (human)
Molecular weightTheoretical: 29.525842 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 KH EEEEAKA EREKKEKEQK EKDK

UniProtKB: Proteasome subunit alpha type-4

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Macromolecule #4: Proteasome subunit alpha type-5

MacromoleculeName: Proteasome subunit alpha type-5 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
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-5

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Macromolecule #5: Proteasome subunit alpha type-1

MacromoleculeName: Proteasome subunit alpha type-1 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.595627 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 RTYLERHMSE FMECNLNELV KHGLRALRET LPAEQDLTTK NVSIGIVGKD LEFTIYDDDD VSPFLEGLEE RP QRKAQPA QPADEPAEKA DEPMEH

UniProtKB: Proteasome subunit alpha type-1

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Macromolecule #6: Proteasome subunit alpha type-3

MacromoleculeName: Proteasome subunit alpha type-3 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.338057 KDa
SequenceString: SSIGTGYDLS ASTFSPDGRV FQVEYAMKAV ENSSTAIGIR CKDGVVFGVE KLVLSKLYEE GSNKRLFNVD RHVGMAVAGL LADARSLAD IAREEASNFR SNFGYNIPLK HLADRVAMYV HAYTLYSAVR PFGCSFMLGS YSVNDGAQLY MIDPSGVSYG Y WGCAIGKA ...String:
SSIGTGYDLS ASTFSPDGRV FQVEYAMKAV ENSSTAIGIR CKDGVVFGVE KLVLSKLYEE GSNKRLFNVD RHVGMAVAGL LADARSLAD IAREEASNFR SNFGYNIPLK HLADRVAMYV HAYTLYSAVR PFGCSFMLGS YSVNDGAQLY MIDPSGVSYG Y WGCAIGKA RQAAKTEIEK LQMKEMTCRD IVKEVAKIIY IVHDEVKDKA FELELSWVGE LTNGRHEIVP KDIREEAEKY AK ESLKEED ESDDDNM

UniProtKB: Proteasome subunit alpha type-3

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Macromolecule #7: Proteasome subunit beta type-3

MacromoleculeName: Proteasome subunit beta type-3 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.841701 KDa
SequenceString: SIMSYNGGAV MAMKGKNCVA IAADRRFGIQ AQMVTTDFQK IFPMGDRLYI GLAGLATDVQ TVAQRLKFRL NLYELKEGRQ IKPYTLMSM VANLLYEKRF GPYYTEPVIA GLDPKTFKPF ICSLDLIGCP MVTDDFVVSG TCAEQMYGMC ESLWEPNMDP D HLFETISQ ...String:
SIMSYNGGAV MAMKGKNCVA IAADRRFGIQ AQMVTTDFQK IFPMGDRLYI GLAGLATDVQ TVAQRLKFRL NLYELKEGRQ IKPYTLMSM VANLLYEKRF GPYYTEPVIA GLDPKTFKPF ICSLDLIGCP MVTDDFVVSG TCAEQMYGMC ESLWEPNMDP D HLFETISQ AMLNAVDRDA VSGMGVIVHI IEKDKITTRT LKARMD

UniProtKB: Proteasome subunit beta type-3

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Macromolecule #8: Proteasome subunit beta type-2

MacromoleculeName: Proteasome subunit beta type-2 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.864277 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 SVRIIDKNGI HDLDNISFPK QGS

UniProtKB: Proteasome subunit beta type-2

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Macromolecule #9: Proteasome subunit beta type-1

MacromoleculeName: Proteasome subunit beta type-1 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.578986 KDa
SequenceString: RFSPYVFNGG TILAIAGEDF AIVASDTRLS EGFSIHTRDS PKCYKLTDKT VIGCSGFHGD CLTLTKIIEA RLKMYKHSNN KAMTTGAIA AMLSTILYSR RFFPYYVYNI IGGLDEEGKG AVYSFDPVGS YQRDSFKAGG SASAMLQPLL DNQVGFKNMQ N VEHVPLSL ...String:
RFSPYVFNGG TILAIAGEDF AIVASDTRLS EGFSIHTRDS PKCYKLTDKT VIGCSGFHGD CLTLTKIIEA RLKMYKHSNN KAMTTGAIA AMLSTILYSR RFFPYYVYNI IGGLDEEGKG AVYSFDPVGS YQRDSFKAGG SASAMLQPLL DNQVGFKNMQ N VEHVPLSL DRAMRLVKDV FISAAERDVY TGDALRICIV TKEGIREETV SLRKD

UniProtKB: Proteasome subunit beta type-1

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Macromolecule #10: Proteasome subunit beta type-4

MacromoleculeName: Proteasome subunit beta type-4 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.41474 KDa
SequenceString: TQNPMVTGTS VLGVKFEGGV VIAADMLGSY GSLARFRNIS RIMRVNNSTM LGASGDYADF QYLKQVLGQM VIDEELLGDG HSYSPRAIH SWLTRAMYSR RSKMNPLWNT MVIGGYADGE SFLGYVDMLG VAYEAPSLAT GYGAYLAQPL LREVLEKQPV L SQTEARDL ...String:
TQNPMVTGTS VLGVKFEGGV VIAADMLGSY GSLARFRNIS RIMRVNNSTM LGASGDYADF QYLKQVLGQM VIDEELLGDG HSYSPRAIH SWLTRAMYSR RSKMNPLWNT MVIGGYADGE SFLGYVDMLG VAYEAPSLAT GYGAYLAQPL LREVLEKQPV L SQTEARDL VERCMRVLYY RDARSYNRFQ IATVTEKGVE IEGPLSTETN WDIAHMISGF E

UniProtKB: Proteasome subunit beta type-4

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Macromolecule #11: Proteasome subunit alpha type-7

MacromoleculeName: Proteasome subunit alpha type-7 / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.929891 KDa
SequenceString: MSYDRAITVF SPDGHLFQVE YAQEAVKKGS TAVGVRGRDI VVLGVEKKSV AKLQDERTVR KICALDDNVC MAFAGLTADA RIVINRARV ECQSHRLTVE DPVTVEYITR YIASLKQRYT QSNGRRPFGI SALIVGFDFD GTPRLYQTDP SGTYHAWKAN A IGRGAKSV ...String:
MSYDRAITVF SPDGHLFQVE YAQEAVKKGS TAVGVRGRDI VVLGVEKKSV AKLQDERTVR KICALDDNVC MAFAGLTADA RIVINRARV ECQSHRLTVE DPVTVEYITR YIASLKQRYT QSNGRRPFGI SALIVGFDFD GTPRLYQTDP SGTYHAWKAN A IGRGAKSV REFLEKNYTD EAIETDDLTI KLVIKALLEV VQSGGKNIEL AVMRRDQSLK ILNPEEIEKY VAEIEKEKEE NE KKKQKKA S

UniProtKB: Proteasome subunit alpha type-7

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Macromolecule #12: Proteasome subunit beta type-6

MacromoleculeName: Proteasome subunit beta type-6 / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.921836 KDa
SequenceString: TTIMAVQFDG GVVLGADSRT TTGSYIANRV TDKLTPIHDR IFCCRSGSAA DTQAVADAVT YQLGFHSIEL NEPPLVHTAA SLFKEMCYR YREDLMAGII IAGWDPQEGG QVYSVPMGGM MVRQSFAIGG SGSSYIYGYV DATYREGMTK EECLQFTANA L ALAMERDG ...String:
TTIMAVQFDG GVVLGADSRT TTGSYIANRV TDKLTPIHDR IFCCRSGSAA DTQAVADAVT YQLGFHSIEL NEPPLVHTAA SLFKEMCYR YREDLMAGII IAGWDPQEGG QVYSVPMGGM MVRQSFAIGG SGSSYIYGYV DATYREGMTK EECLQFTANA L ALAMERDG SSGGVIRLAA IAESGVERQV LLGDQIPKFA VATLPPA

UniProtKB: Proteasome subunit beta type-6

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Macromolecule #13: Proteasome subunit beta type-7

MacromoleculeName: Proteasome subunit beta type-7 / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.32198 KDa
SequenceString: TTIAGVVYKD GIVLGADTRA TEGMVVADKN CSKIHFISPN IYCCGAGTAA DTDMTTQLIS SNLELHSLST GRLPRVVTAN RMLKQMLFR YQGYIGAALV LGGVDVTGPH LYSIYPHGST DKLPYVTMGS GSLAAMAVFE DKFRPDMEEE EAKNLVSEAI A AGIFNDLG ...String:
TTIAGVVYKD GIVLGADTRA TEGMVVADKN CSKIHFISPN IYCCGAGTAA DTDMTTQLIS SNLELHSLST GRLPRVVTAN RMLKQMLFR YQGYIGAALV LGGVDVTGPH LYSIYPHGST DKLPYVTMGS GSLAAMAVFE DKFRPDMEEE EAKNLVSEAI A AGIFNDLG SGSNIDLCVI SKNKLDFLRP YTVPNKKGTR LGRYRCEKGT TAVLTEKITP LEIEVLEETV QTMDTS

UniProtKB: Proteasome subunit beta type-7

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Macromolecule #14: Proteasome subunit beta type-5

MacromoleculeName: Proteasome subunit beta type-5 / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.484369 KDa
SequenceString: TTTLAFKFRH GVIVAADSRA TAGAYIASQT VKKVIEINPY LLGTMAGGAA DCSFWERLLA RQCRIYELRN KERISVAAAS KLLANMVYQ YKGMGLSMGT MICGWDKRGP GLYYVDSEGN RISGATFSVG SGSVYAYGVM DRGYSYDLEV EQAYDLARRA I YQATYRDA ...String:
TTTLAFKFRH GVIVAADSRA TAGAYIASQT VKKVIEINPY LLGTMAGGAA DCSFWERLLA RQCRIYELRN KERISVAAAS KLLANMVYQ YKGMGLSMGT MICGWDKRGP GLYYVDSEGN RISGATFSVG SGSVYAYGVM DRGYSYDLEV EQAYDLARRA I YQATYRDA YSGGAVNLYH VREDGWIRVS SDNVADLHEK YSGSTP

UniProtKB: Proteasome subunit beta type-5

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Macromolecule #15: (3AR,6R,6AS)-6-((S)-((S)-CYCLOHEX-2-ENYL)(HYDROXY)METHYL)-6A-METH...

MacromoleculeName: (3AR,6R,6AS)-6-((S)-((S)-CYCLOHEX-2-ENYL)(HYDROXY)METHYL)-6A-METHYL-4-OXO-HEXAHYDRO-2H-FURO[3,2-C]PYRROLE-6-CARBALDEHYDE
type: ligand / ID: 15 / Number of copies: 6 / Formula: SA1
Molecular weightTheoretical: 279.332 Da
Chemical component information

ChemComp-SA1:
(3AR,6R,6AS)-6-((S)-((S)-CYCLOHEX-2-ENYL)(HYDROXY)METHYL)-6A-METHYL-4-OXO-HEXAHYDRO-2H-FURO[3,2-C]PYRROLE-6-CARBALDEHYDE

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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 / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3+) / Number images used: 209737
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3+)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3+)
FSC plot (resolution estimation)

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