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- EMDB-54027: CryoEM structure of human 20S proteasome in complex with proteaso... -

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Basic information

Entry
Database: EMDB / ID: EMD-54027
TitleCryoEM structure of human 20S proteasome in complex with proteasome inhibitor CP-17
Map dataPrimary map after y-flip and EMReady sharpening.
Sample
  • Organelle or cellular component: CryoEM structure of human 20S proteasome in complex with proteasome inhibitor CP-17
    • Protein or peptide: x 14 types
  • Ligand: x 1 types
KeywordsHYDROLASE
Function / homology
Function and homology information


purine ribonucleoside triphosphate binding / Antigen processing: Ub, ATP-independent proteasomal degradation / sperm glycocalyx / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / proteasome core complex / perinuclear theca / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / myofibril ...purine ribonucleoside triphosphate binding / Antigen processing: Ub, ATP-independent proteasomal degradation / sperm glycocalyx / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / proteasome core complex / perinuclear theca / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / myofibril / proteasomal ubiquitin-independent protein catabolic process / sperm head-tail coupling apparatus / immune system process / proteasome endopeptidase complex / NF-kappaB binding / proteasome core complex, beta-subunit complex / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteasome assembly / : / ciliary tip / proteasome complex / sarcomere / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / centriole / APC/C:Cdc20 mediated degradation of Securin / sperm end piece / negative regulation of inflammatory response to antigenic stimulus / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / lipopolysaccharide binding / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / P-body / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of DVL / Degradation of AXIN / Degradation of CRY and PER proteins / Hh mutants are degraded by ERAD / Activation of NF-kappaB in B cells / G2/M Checkpoints / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / Regulation of RUNX3 expression and activity / Autodegradation of the E3 ubiquitin ligase COP1 / Defective CFTR causes cystic fibrosis / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Hedgehog 'on' state / Vif-mediated degradation of APOBEC3G / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / MAPK6/MAPK4 signaling / Degradation of CDH1 / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / CDK-mediated phosphorylation and removal of Cdc6 / ABC-family protein mediated transport / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / response to virus / FCERI mediated NF-kB activation / nuclear matrix / Regulation of expression of SLITs and ROBOs / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RUNX2 expression and activity / Regulation of RAS by GAPs / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / UCH proteinases / KEAP1-NFE2L2 pathway / peptidase activity / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / sperm principal piece / RUNX1 regulates transcription of genes involved in differentiation of HSCs / ER-Phagosome pathway / Neddylation / regulation of inflammatory response / response to oxidative stress / sperm midpiece / secretory granule lumen / endopeptidase activity / ficolin-1-rich granule lumen / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / Ub-specific processing proteases / cilium / nuclear body
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 alpha5 / Proteasome subunit alpha6 / 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 alpha5 / Proteasome subunit alpha6 / 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: 2.95 Å
AuthorsBenova V / Suelzen H / Boura E / Silhan J / Fajtova P
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: CryoEM structure of human 20S proteasome in complex with proteasome inhibitor CP-17
Authors: Benova V / Suelzen H / Boura E / Silhan J / Fajtova P
History
DepositionJun 15, 2025-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54027.png

Downloads & links

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Map

FileDownload / File: emd_54027.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary map after y-flip and EMReady sharpening.
Projections & slices

Image control

Size
Brightness
Contrast
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8336 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.0
Minimum - Maximum-0.46314114 - 22.961489
Average (Standard dev.)0.055272836 (±0.8660322)
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_54027_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Final, unsharpened reconstruction after y-flip

Fileemd_54027_additional_1.map
AnnotationFinal, unsharpened reconstruction after y-flip
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Y-flipped half map A

Fileemd_54027_half_map_1.map
AnnotationY-flipped half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Y-flipped half map B

Fileemd_54027_half_map_2.map
AnnotationY-flipped half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CryoEM structure of human 20S proteasome in complex with proteaso...

EntireName: CryoEM structure of human 20S proteasome in complex with proteasome inhibitor CP-17
Components
  • Organelle or cellular component: CryoEM structure of human 20S proteasome in complex with proteasome inhibitor CP-17
    • 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: ~{N}-[(2~{S})-3-(1~{H}-indol-3-yl)-1-[[(2~{S})-3-(1~{H}-indol-3-yl)-1-[[(2~{S},3~{R},4~{S})-4-methyl-3,5-bis(oxidanyl)-1-phenyl-pentan-2-yl]amino]-1-oxidanylidene-propan-2-yl]amino]-1-oxidanylidene-propan-2-yl]hexanamide

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Supramolecule #1: CryoEM structure of human 20S proteasome in complex with proteaso...

SupramoleculeName: CryoEM structure of human 20S proteasome in complex with proteasome inhibitor CP-17
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#14
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
Recombinant expressionOrganism: Homo sapiens environmental sample (environmental samples)
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 / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.927535 KDa
Recombinant expressionOrganism: Homo sapiens environmental sample (environmental samples)
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-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
Recombinant expressionOrganism: Homo sapiens environmental sample (environmental samples)
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
Recombinant expressionOrganism: Homo sapiens environmental sample (environmental samples)
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
Recombinant expressionOrganism: Homo sapiens environmental sample (environmental samples)
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 / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.469252 KDa
Recombinant expressionOrganism: Homo sapiens environmental sample (environmental samples)
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 ELTNGRHEIV PKDIREEAEK YA KESLKEE DESDDDNM

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
Recombinant expressionOrganism: Homo sapiens environmental sample (environmental samples)
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
Recombinant expressionOrganism: Homo sapiens environmental sample (environmental samples)
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
Recombinant expressionOrganism: Homo sapiens environmental sample (environmental samples)
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
Recombinant expressionOrganism: Homo sapiens environmental sample (environmental samples)
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
Recombinant expressionOrganism: Homo sapiens environmental sample (environmental samples)
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
Recombinant expressionOrganism: Homo sapiens environmental sample (environmental samples)
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
Recombinant expressionOrganism: Homo sapiens environmental sample (environmental samples)
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: 22.14202 KDa
Recombinant expressionOrganism: Homo sapiens environmental sample (environmental samples)
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 YS

UniProtKB: Proteasome subunit beta type-5

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Macromolecule #15: ~{N}-[(2~{S})-3-(1~{H}-indol-3-yl)-1-[[(2~{S})-3-(1~{H}-indol-3-y...

MacromoleculeName: ~{N}-[(2~{S})-3-(1~{H}-indol-3-yl)-1-[[(2~{S})-3-(1~{H}-indol-3-yl)-1-[[(2~{S},3~{R},4~{S})-4-methyl-3,5-bis(oxidanyl)-1-phenyl-pentan-2-yl]amino]-1-oxidanylidene-propan-2-yl]amino]-1- ...Name: ~{N}-[(2~{S})-3-(1~{H}-indol-3-yl)-1-[[(2~{S})-3-(1~{H}-indol-3-yl)-1-[[(2~{S},3~{R},4~{S})-4-methyl-3,5-bis(oxidanyl)-1-phenyl-pentan-2-yl]amino]-1-oxidanylidene-propan-2-yl]amino]-1-oxidanylidene-propan-2-yl]hexanamide
type: ligand / ID: 15 / Number of copies: 2 / Formula: A1JHK
Molecular weightTheoretical: 679.848 Da

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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

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPES4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid
50.0 mMNaClsodium chloride
0.25 mMTHPTris(hydroxypropyl)phosphine
VitrificationCryogen name: ETHANE / Chamber humidity: 0 % / Instrument: FEI VITROBOT MARK IV
Details50 micromolar CP-17

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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: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9hmn

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 254452
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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