[English] 日本語
Yorodumi
- EMDB-75334: 20S Alpha 3 Deletion proteasome core particle in complex with Fub... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-75334
Title20S Alpha 3 Deletion proteasome core particle in complex with Fub1 and Blm10
Map dataFinal Sharpened for 20S Alpha 3 Deletion proteasome core particle in complex with Fub1 and Blm10
Sample
  • Complex: C2 symmetry expanded and subtracted 20S Proteasome, Blm10, Fub1 Complex Halfmer
    • Protein or peptide: x 15 types
Keywords20S Proteasome / Proteasome Regulator / Proteasome Inhibitor / HYDROLASE
Function / homology
Function and homology information


proteasome core complex import into nucleus / proteasome storage granule assembly / ER-Phagosome pathway / Antigen processing: Ub, ATP-independent proteasomal degradation / Regulation of PTEN stability and activity / proteasome core complex assembly / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Proteasome assembly / CDK-mediated phosphorylation and removal of Cdc6 ...proteasome core complex import into nucleus / proteasome storage granule assembly / ER-Phagosome pathway / Antigen processing: Ub, ATP-independent proteasomal degradation / Regulation of PTEN stability and activity / proteasome core complex assembly / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Proteasome assembly / CDK-mediated phosphorylation and removal of Cdc6 / nuclear outer membrane-endoplasmic reticulum membrane network / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / peptidase activator activity / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / KEAP1-NFE2L2 pathway / Neddylation / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome binding / Antigen processing: Ubiquitination & Proteasome degradation / Ub-specific processing proteases / proteasomal ubiquitin-independent protein catabolic process / proteasome storage granule / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / endopeptidase activator activity / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteasome assembly / Neutrophil degranulation / proteasome complex / regulation of proteasomal protein catabolic process / peroxisome / chromatin organization / endopeptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA repair / mRNA binding / DNA damage response / endoplasmic reticulum membrane / mitochondrion / nucleus / cytosol
Similarity search - Function
PI31 proteasome regulator, C-terminal / PI31 proteasome regulator / Proteasome activator Blm10, N-terminal / Proteasome-substrate-size regulator, N-terminal / Proteasome activator complex subunit 4 C-terminal domain / Proteasome activator Blm10, mid region / Proteasome activator complex subunit 4 / : / Proteasome activator complex subunit 4-like, C-terminal / Proteasome activator complex subunit 4, mid HEAT repeats region ...PI31 proteasome regulator, C-terminal / PI31 proteasome regulator / Proteasome activator Blm10, N-terminal / Proteasome-substrate-size regulator, N-terminal / Proteasome activator complex subunit 4 C-terminal domain / Proteasome activator Blm10, mid region / Proteasome activator complex subunit 4 / : / Proteasome activator complex subunit 4-like, C-terminal / Proteasome activator complex subunit 4, mid HEAT repeats region / Proteasome activator complex subunit 4-like, HEAT repeat-like / 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 / Armadillo-type fold
Similarity search - Domain/homology
Probable proteasome subunit alpha type-7 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-6 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 / Silencing boundary-establishment protein FUB1 / Proteasome subunit beta type-5 / Proteasome subunit beta type-7 ...Probable proteasome subunit alpha type-7 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-6 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 / Silencing boundary-establishment protein FUB1 / Proteasome subunit beta type-5 / Proteasome subunit beta type-7 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-6 / Proteasome subunit alpha type-4 / Proteasome activator BLM10
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsWalsh Jr RM / Rawson S / Fermin Perez E / Venclovaite U / Hanna J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM144367 United States
CitationJournal: To Be Published
Title: Blm10 and PI31 Compromise a Failsafe Mechanism for Proteasome Inhibition
Authors: Darlene F / Rawson S / Walsh Jr RM / Fermin Perez E / Venclovaite U / Velez B / Rajakumar T / Hanna J
History
DepositionJan 29, 2026-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_75334.png

Downloads & links

-
Map

FileDownload / File: emd_75334.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal Sharpened for 20S Alpha 3 Deletion proteasome core particle in complex with Fub1 and Blm10
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.19 Å/pix.
x 480 pix.
= 571.2 Å		1.19 Å/pix.
x 480 pix.
= 571.2 Å		1.19 Å/pix.
x 480 pix.
= 571.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.19 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00265
Minimum - Maximum-0.036744982 - 0.057891406
Average (Standard dev.)0.000049482784 (±0.0012816825)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 571.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Final Unsharpened for 20S Alpha 3 Deletion proteasome...

Fileemd_75334_additional_1.map
AnnotationFinal Unsharpened for 20S Alpha 3 Deletion proteasome core particle in complex with Fub1 and Blm10
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map 1 for 20S Alpha 3 Deletion...

Fileemd_75334_half_map_1.map
AnnotationHalf Map 1 for 20S Alpha 3 Deletion proteasome core particle in complex with Fub1 and Blm10
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map 2 for 20S Alpha 3 Deletion...

Fileemd_75334_half_map_2.map
AnnotationHalf Map 2 for 20S Alpha 3 Deletion proteasome core particle in complex with Fub1 and Blm10
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : C2 symmetry expanded and subtracted 20S Proteasome, Blm10, Fub1 C...

EntireName: C2 symmetry expanded and subtracted 20S Proteasome, Blm10, Fub1 Complex Halfmer
Components
  • Complex: C2 symmetry expanded and subtracted 20S Proteasome, Blm10, Fub1 Complex Halfmer
    • Protein or peptide: Proteasome subunit alpha type-1
    • Protein or peptide: Proteasome subunit alpha type-2
    • Protein or peptide: Proteasome subunit alpha type-6
    • Protein or peptide: Proteasome subunit alpha type-7
    • Protein or peptide: Proteasome subunit beta type-1
    • Protein or peptide: Proteasome subunit beta type-2
    • Protein or peptide: Proteasome subunit beta type-3
    • Protein or peptide: Proteasome subunit beta type-4
    • Protein or peptide: Proteasome subunit beta type-5
    • Protein or peptide: Proteasome subunit beta type-6
    • Protein or peptide: Proteasome subunit beta type-7
    • Protein or peptide: Proteasome subunit alpha type-4
    • Protein or peptide: Proteasome activator BLM10
    • Protein or peptide: Proteasome subunit alpha type-5
    • Protein or peptide: Silencing boundary-establishment protein FUB1

+
Supramolecule #1: C2 symmetry expanded and subtracted 20S Proteasome, Blm10, Fub1 C...

SupramoleculeName: C2 symmetry expanded and subtracted 20S Proteasome, Blm10, Fub1 Complex Halfmer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 240 KDa

+
Macromolecule #1: Proteasome subunit alpha type-1

MacromoleculeName: Proteasome subunit alpha type-1 / type: protein_or_peptide / ID: 1 / Details: Proteasome subunit alpha type-1 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 28.03383 KDa
SequenceString: MSGAAAASAA GYDRHITIFS PEGRLYQVEY AFKATNQTNI NSLAVRGKDC TVVISQKKVP DKLLDPTTVS YIFCISRTIG MVVNGPIPD ARNAALRAKA EAAEFRYKYG YDMPCDVLAK RMANLSQIYT QRAYMRPLGV ILTFVSVDEE LGPSIYKTDP A GYYVGYKA ...String:
MSGAAAASAA GYDRHITIFS PEGRLYQVEY AFKATNQTNI NSLAVRGKDC TVVISQKKVP DKLLDPTTVS YIFCISRTIG MVVNGPIPD ARNAALRAKA EAAEFRYKYG YDMPCDVLAK RMANLSQIYT QRAYMRPLGV ILTFVSVDEE LGPSIYKTDP A GYYVGYKA TATGPKQQEI TTNLENHFKK SKIDHINEES WEKVVEFAIT HMIDALGTEF SKNDLEVGVA TKDKFFTLSA EN IEERLVA IAEQD

UniProtKB: Proteasome subunit alpha type-1

+
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: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 27.191828 KDa
SequenceString: MTDRYSFSLT TFSPSGKLGQ IDYALTAVKQ GVTSLGIKAT NGVVIATEKK SSSPLAMSET LSKVSLLTPD IGAVYSGMGP DYRVLVDKS RKVAHTSYKR IYGEYPPTKL LVSEVAKIMQ EATQSGGVRP FGVSLLIAGH DEFNGFSLYQ VDPSGSYFPW K ATAIGKGS ...String:
MTDRYSFSLT TFSPSGKLGQ IDYALTAVKQ GVTSLGIKAT NGVVIATEKK SSSPLAMSET LSKVSLLTPD IGAVYSGMGP DYRVLVDKS RKVAHTSYKR IYGEYPPTKL LVSEVAKIMQ EATQSGGVRP FGVSLLIAGH DEFNGFSLYQ VDPSGSYFPW K ATAIGKGS VAAKTFLEKR WNDELELEDA IHIALLTLKE SVEGEFNGDT IELAIIGDEN PDLLGYTGIP TDKGPRFRKL TS QEINDRL EAL

UniProtKB: Proteasome subunit alpha type-2

+
Macromolecule #3: Proteasome subunit alpha type-6

MacromoleculeName: Proteasome subunit alpha type-6 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 25.634 KDa
SequenceString: MFRNNYDGDT VTFSPTGRLF QVEYALEAIK QGSVTVGLRS NTHAVLVALK RNADELSSYQ KKIIKCDEHM GLSLAGLAPD ARVLSNYLR QQCNYSSLVF NRKLAVERAG HLLCDKAQKN TQSYGGRPYG VGLLIIGYDK SGAHLLEFQP SGNVTELYGT A IGARSQGA ...String:
MFRNNYDGDT VTFSPTGRLF QVEYALEAIK QGSVTVGLRS NTHAVLVALK RNADELSSYQ KKIIKCDEHM GLSLAGLAPD ARVLSNYLR QQCNYSSLVF NRKLAVERAG HLLCDKAQKN TQSYGGRPYG VGLLIIGYDK SGAHLLEFQP SGNVTELYGT A IGARSQGA KTYLERTLDT FIKIDGNPDE LIKAGVEAIS QSLRDESLTV DNLSIAIVGK DTPFTIYDGE AVAKYI

UniProtKB: Proteasome subunit alpha type-6

+
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: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 31.575068 KDa
SequenceString: MTSIGTGYDL SNSVFSPDGR NFQVEYAVKA VENGTTSIGI KCNDGVVFAV EKLITSKLLV PQKNVKIQVV DRHIGCVYSG LIPDGRHLV NRGREEAASF KKLYKTPIPI PAFADRLGQY VQAHTLYNSV RPFGVSTIFG GVDKNGAHLY MLEPSGSYWG Y KGAATGKG ...String:
MTSIGTGYDL SNSVFSPDGR NFQVEYAVKA VENGTTSIGI KCNDGVVFAV EKLITSKLLV PQKNVKIQVV DRHIGCVYSG LIPDGRHLV NRGREEAASF KKLYKTPIPI PAFADRLGQY VQAHTLYNSV RPFGVSTIFG GVDKNGAHLY MLEPSGSYWG Y KGAATGKG RQSAKAELEK LVDHHPEGLS AREAVKQAAK IIYLAHEDNK EKDFELEISW CSLSETNGLH KFVKGDLLQE AI DFAQKEI NGDDDEDEDD SDNVMSSDDE NAPVATNANA TTDQEGDIHL E

UniProtKB: Probable proteasome subunit alpha type-7

+
Macromolecule #5: Proteasome subunit beta type-1

MacromoleculeName: Proteasome subunit beta type-1 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 23.573604 KDa
SequenceString: MNGIQVDINR LKKGEVSLGT SIMAVTFKDG VILGADSRTT TGAYIANRVT DKLTRVHDKI WCCRSGSAAD TQAIADIVQY HLELYTSQY GTPSTETAAS VFKELCYENK DNLTAGIIVA GYDDKNKGEV YTIPLGGSVH KLPYAIAGSG STFIYGYCDK N FRENMSKE ...String:
MNGIQVDINR LKKGEVSLGT SIMAVTFKDG VILGADSRTT TGAYIANRVT DKLTRVHDKI WCCRSGSAAD TQAIADIVQY HLELYTSQY GTPSTETAAS VFKELCYENK DNLTAGIIVA GYDDKNKGEV YTIPLGGSVH KLPYAIAGSG STFIYGYCDK N FRENMSKE ETVDFIKHSL SQAIKWDGSS GGVIRMVVLT AAGVERLIFY PDEYEQL

UniProtKB: Proteasome subunit beta type-1

+
Macromolecule #6: Proteasome subunit beta type-2

MacromoleculeName: Proteasome subunit beta type-2 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 28.299889 KDa
SequenceString: MAGLSFDNYQ RNNFLAENSH TQPKATSTGT TIVGVKFNNG VVIAADTRST QGPIVADKNC AKLHRISPKI WCAGAGTAAD TEAVTQLIG SNIELHSLYT SREPRVVSAL QMLKQHLFKY QGHIGAYLIV AGVDPTGSHL FSIHAHGSTD VGYYLSLGSG S LAAMAVLE ...String:
MAGLSFDNYQ RNNFLAENSH TQPKATSTGT TIVGVKFNNG VVIAADTRST QGPIVADKNC AKLHRISPKI WCAGAGTAAD TEAVTQLIG SNIELHSLYT SREPRVVSAL QMLKQHLFKY QGHIGAYLIV AGVDPTGSHL FSIHAHGSTD VGYYLSLGSG S LAAMAVLE SHWKQDLTKE EAIKLASDAI QAGIWNDLGS GSNVDVCVME IGKDAEYLRN YLTPNVREEK QKSYKFPRGT TA VLKESIV NICDIQEEQV DITA

UniProtKB: Proteasome subunit beta type-2

+
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: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 22.627842 KDa
SequenceString: MSDPSSINGG IVVAMTGKDC VAIACDLRLG SQSLGVSNKF EKIFHYGHVF LGITGLATDV TTLNEMFRYK TNLYKLKEER AIEPETFTQ LVSSSLYERR FGPYFVGPVV AGINSKSGKP FIAGFDLIGC IDEAKDFIVS GTASDQLFGM CESLYEPNLE P EDLFETIS ...String:
MSDPSSINGG IVVAMTGKDC VAIACDLRLG SQSLGVSNKF EKIFHYGHVF LGITGLATDV TTLNEMFRYK TNLYKLKEER AIEPETFTQ LVSSSLYERR FGPYFVGPVV AGINSKSGKP FIAGFDLIGC IDEAKDFIVS GTASDQLFGM CESLYEPNLE P EDLFETIS QALLNAADRD ALSGWGAVVY IIKKDEVVKR YLKMRQD

UniProtKB: Proteasome subunit beta type-3

+
Macromolecule #8: Proteasome subunit beta type-4

MacromoleculeName: Proteasome subunit beta type-4 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 22.545676 KDa
SequenceString: MDIILGIRVQ DSVILASSKA VTRGISVLKD SDDKTRQLSP HTLMSFAGEA GDTVQFAEYI QANIQLYSIR EDYELSPQAV SSFVRQELA KSIRSRRPYQ VNVLIGGYDK KKNKPELYQI DYLGTKVELP YGAHGYSGFY TFSLLDHHYR PDMTTEEGLD L LKLCVQEL ...String:
MDIILGIRVQ DSVILASSKA VTRGISVLKD SDDKTRQLSP HTLMSFAGEA GDTVQFAEYI QANIQLYSIR EDYELSPQAV SSFVRQELA KSIRSRRPYQ VNVLIGGYDK KKNKPELYQI DYLGTKVELP YGAHGYSGFY TFSLLDHHYR PDMTTEEGLD L LKLCVQEL EKRMPMDFKG VIVKIVDKDG IRQVDDFQAQ

UniProtKB: Proteasome subunit beta type-4

+
Macromolecule #9: Proteasome subunit beta type-5

MacromoleculeName: Proteasome subunit beta type-5 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 31.670539 KDa
SequenceString: MQAIADSFSV PNRLVKELQY DNEQNLESDF VTGASQFQRL APSLTVPPIA SPQQFLRAHT DDSRNPDCKI KIAHGTTTLA FRFQGGIIV AVDSRATAGN WVASQTVKKV IEINPFLLGT MAGGAADCQF WETWLGSQCR LHELREKERI SVAAASKILS N LVYQYKGA ...String:
MQAIADSFSV PNRLVKELQY DNEQNLESDF VTGASQFQRL APSLTVPPIA SPQQFLRAHT DDSRNPDCKI KIAHGTTTLA FRFQGGIIV AVDSRATAGN WVASQTVKKV IEINPFLLGT MAGGAADCQF WETWLGSQCR LHELREKERI SVAAASKILS N LVYQYKGA GLSMGTMICG YTRKEGPTIY YVDSDGTRLK GDIFCVGSGQ TFAYGVLDSN YKWDLSVEDA LYLGKRSILA AA HRDAYSG GSVNLYHVTE DGWIYHGNHD VGELFWKVKE EEGSFNNVIG

UniProtKB: Proteasome subunit beta type-5

+
Macromolecule #10: Proteasome subunit beta type-6

MacromoleculeName: Proteasome subunit beta type-6 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 26.905076 KDa
SequenceString: MATIASEYSS EASNTPIEHQ FNPYGDNGGT ILGIAGEDFA VLAGDTRNIT DYSINSRYEP KVFDCGDNIV MSANGFAADG DALVKRFKN SVKWYHFDHN DKKLSINSAA RNIQHLLYGK RFFPYYVHTI IAGLDEDGKG AVYSFDPVGS YEREQCRAGG A AASLIMPF ...String:
MATIASEYSS EASNTPIEHQ FNPYGDNGGT ILGIAGEDFA VLAGDTRNIT DYSINSRYEP KVFDCGDNIV MSANGFAADG DALVKRFKN SVKWYHFDHN DKKLSINSAA RNIQHLLYGK RFFPYYVHTI IAGLDEDGKG AVYSFDPVGS YEREQCRAGG A AASLIMPF LDNQVNFKNQ YEPGTNGKVK KPLKYLSVEE VIKLVRDSFT SATERHIQVG DGLEILIVTK DGVRKEFYEL KR D

UniProtKB: Proteasome subunit beta type-6

+
Macromolecule #11: Proteasome subunit beta type-7

MacromoleculeName: Proteasome subunit beta type-7 / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 29.471289 KDa
SequenceString: MNHDPFSWGR PADSTYGAYN TQIANAGASP MVNTQQPIVT GTSVISMKYD NGVIIAADNL GSYGSLLRFN GVERLIPVGD NTVVGISGD ISDMQHIERL LKDLVTENAY DNPLADAEEA LEPSYIFEYL ATVMYQRRSK MNPLWNAIIV AGVQSNGDQF L RYVNLLGV ...String:
MNHDPFSWGR PADSTYGAYN TQIANAGASP MVNTQQPIVT GTSVISMKYD NGVIIAADNL GSYGSLLRFN GVERLIPVGD NTVVGISGD ISDMQHIERL LKDLVTENAY DNPLADAEEA LEPSYIFEYL ATVMYQRRSK MNPLWNAIIV AGVQSNGDQF L RYVNLLGV TYSSPTLATG FGAHMANPLL RKVVDRESDI PKTTVQVAEE AIVNAMRVLY YRDARSSRNF SLAIIDKNTG LT FKKNLQV ENMKWDFAKD IKGYGTQKI

UniProtKB: Proteasome subunit beta type-7

+
Macromolecule #12: Proteasome subunit alpha type-4

MacromoleculeName: Proteasome subunit alpha type-4 / type: protein_or_peptide / ID: 12 / Number of copies: 4 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 28.478111 KDa
SequenceString: MSGYDRALSI FSPDGHIFQV EYALEAVKRG TCAVGVKGKN CVVLGCERRS TLKLQDTRIT PSKVSKIDSH VVLSFSGLNA DSRILIEKA RVEAQSHRLT LEDPVTVEYL TRYVAGVQQR YTQSGGVRPF GVSTLIAGFD PRDDEPKLYQ TEPSGIYSSW S AQTIGRNS ...String:
MSGYDRALSI FSPDGHIFQV EYALEAVKRG TCAVGVKGKN CVVLGCERRS TLKLQDTRIT PSKVSKIDSH VVLSFSGLNA DSRILIEKA RVEAQSHRLT LEDPVTVEYL TRYVAGVQQR YTQSGGVRPF GVSTLIAGFD PRDDEPKLYQ TEPSGIYSSW S AQTIGRNS KTVREFLEKN YDRKEPPATV EECVKLTVRS LLEVVQTGAK NIEITVVKPD SDIVALSSEE INQYVTQIEQ EK QEQQEQD KKKKSNH

UniProtKB: Proteasome subunit alpha type-4

+
Macromolecule #13: Proteasome activator BLM10

MacromoleculeName: Proteasome activator BLM10 / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 249.243672 KDa
SequenceString: MHHHHHHHHH HHHTANNDDD IKSPMTANND DDIKSPIPIT NKTLSQLKRF ERSPGRPSSS QGEIKRKKSR LYAADGRPHS PLRARSATP TLQDQKLFNG MDSTSLLNER LQHYTLDYVS DRAQHMKNIY DPSSRWFSRS VRPEFPIEEF LPYKTESHED Q AKYLCHVL ...String:
MHHHHHHHHH HHHTANNDDD IKSPMTANND DDIKSPIPIT NKTLSQLKRF ERSPGRPSSS QGEIKRKKSR LYAADGRPHS PLRARSATP TLQDQKLFNG MDSTSLLNER LQHYTLDYVS DRAQHMKNIY DPSSRWFSRS VRPEFPIEEF LPYKTESHED Q AKYLCHVL VNLYIAISSL DIQGLISISS KDLADLKKEV DDLALKTDLF RLSNNTAEND LLGNDIADYD DAEGLEDELD EY FDLAGPD FNATGKITAK SATIVNVNHW TNELKNCLHF DFPVALRKSL ATVYYYLSLV QGQKVYRQMH VDMFERLVSL DDD RTNFTE LLQKQGLLLD HQIMLNFLCE FLPYPDPDYA RYELSSKEDL QLFRLLLKHA HNAKPFFDKS KESLLVDTMN FLLS SLAPS TMMAVMPIVT SVVPYHYHIH SKIIDYFPFC YSIWSSVSAN VAIDTHMYDF VGSISKDVHN KILSSEHEKD VVGVE FGEF GIFTDDQMTF MFNRLQGHLR TDGQIHSYSR TVKPFVYAIN GSKKDRFFEK LVSLAKAIET FIHPSNNGFW TKPNAK FVH AFIKSYHGRV KYEEDICARG VTNGICLTSF CHEEIVEIFL NIISLGSQNK NPDIANYYIS CFAYLLELDP SNAYLIY DK ILIDLYDTLA DQFINSRHRI ISSLKQFTRV IRFIVMDKLY RVHITNVLSM LVSKLDMNDT NLTSNLINGI VSIAAFIP I QDLTGEDDYI SFESDTLPLV QQHFYHIKCG ESSKTFRVDD ELLNNAFKAS TTVFQSMLKV YVEKIFQLVD VDLEDSLVT KINQTTMILQ ESMDDKIFNY FASLLQRNFW SNDSFKEKDP NYELVTIPLA ALVRRNNGLS KELVRTLLFH IKEQIKRGAG SVRSTSEIQ QRDVKLVLYL TALNDVLRQC HESLLEYSDE LITFMKYLYD NVTNPPLDVI TSIVIHSALA TLCTTEITDC R LFPEDSKI PEKDRWGGLQ FDPRRFDKQH LSFQWHVPSS DEITLSISIL ESLSEYCINN VEELMKAPRH DSEYGDMIQK YV LVMTHTL SGSSLLFDPD FNKYRTQSNL SYREKLILLK NIRENNCDPQ ELDIDIEQIR SGKDDEDYIE SKDIEAGLNA GVS DVVQLR DEFPDELIVD EEVVSEMPSG VNTPIAGTHG TDNSAMSSDL AFRDLDIYTC NYYFGNTTEE KLQNPQYLQV HRVR ARIGH FFHKLYVFLS TNFENNTNMF QILLHGLKVW FTDLGQETVF NEDPNAFIDV DFLENVQSLS HVNEPFTRTN FAIRA NSLH QSRVLLHSTN RKASKLENLL LVDIIQLATS LYPDIYKPAQ GTLVHCMKQL VGSYGVVINK IIPSLEKAIK DHDYMK IQV ILNVLLIKKI HRKLMTDYKD IGRLIFLLIE CCRVNELEIG MYADKILTDI VIGIKIPSSV CVISDQAFLP LAPPDGT IN LQVEAVKLAK KKKREYYLSL LVDLQDKLLD KLDNEKDMGW KIRMFILRFV TQIQSNLESK PDKRAVFSII SQISTKHP E IIHLVVKSLL STCNKIISLS DYEYDITRAY KNEFNPSFVE ILDTSTTSFP KTFTEEMNNF DNPKYFIDLR AYVGWLCWG RLMYVMSPKA LKLNLRENEL EVLKTAGHLL TREFLRDVTM NLVQDNETRG VFSSGNVSFF SLVILLISSG FCELNMSDLF ELCESYYNK DDKASMIMSV EIVAGLVCGS KFMSVSDLDK RDTFIENFLA KCLDYELNHD AFEIWSTLAW WLPAVVDLRR S KTFFCHFI NADGMFDRES DAATHQTSKI YMLRSILMSM EFRAPDVGKL FDELVFDHPY DQVRQAVAKL LTTLVQNQSN PS ISDPTTL LEAERNDPDG LGLPLKSVPE KVDAYIKKQF EIIKNLEDSV VGLNPQQFIK TDYFYRTSTI FYWIKEMARG PNK VLLVPY LVDYVLPFLI GLVKHKDVCA LASLDPVRLY AGLGYMPIRK NHVAAIVDYV CSSNVALSSN QTKLQLAFIQ HFLS AELLQ LTEEEKNKIL EFVVSNLYNE QFVEVRVRAA SILSDIVHNW KEEQPLLSLI ERFAKGLDVN KYTSKERQKL SKTDI KIHG NVLGLGAIIS AFPYVFPLPP WIPKQLSNLS SWARTSGMTG QAAKNTISEF KKVRADTWKF DRASFNTEEL EDLEGV LWR SYYA

UniProtKB: Proteasome activator BLM10

+
Macromolecule #14: Proteasome subunit alpha type-5

MacromoleculeName: Proteasome subunit alpha type-5 / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 28.649086 KDa
SequenceString: MFLTRSEYDR GVSTFSPEGR LFQVEYSLEA IKLGSTAIGI ATKEGVVLGV EKRATSPLLE SDSIEKIVEI DRHIGCAMSG LTADARSMI EHARTAAVTH NLYYDEDINV ESLTQSVCDL ALRFGEGASG EERLMSRPFG VALLIAGHDA DDGYQLFHAE P SGTFYRYN ...String:
MFLTRSEYDR GVSTFSPEGR LFQVEYSLEA IKLGSTAIGI ATKEGVVLGV EKRATSPLLE SDSIEKIVEI DRHIGCAMSG LTADARSMI EHARTAAVTH NLYYDEDINV ESLTQSVCDL ALRFGEGASG EERLMSRPFG VALLIAGHDA DDGYQLFHAE P SGTFYRYN AKAIGSGSEG AQAELLNEWH SSLTLKEAEL LVLKILKQVM EEKLDENNAQ LSCITKQDGF KIYDNEKTAE LI KELKEKE AAESPEEADV EMS

UniProtKB: Proteasome subunit alpha type-5

+
Macromolecule #15: Silencing boundary-establishment protein FUB1

MacromoleculeName: Silencing boundary-establishment protein FUB1 / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 26.780809 KDa
SequenceString: MIENKVELVA ELVLESIGKT EVVSRHTEGT KSCQVSFRIK DSPSEKGSTS FLSELVVIQT LDDNDKYTVV IRHGTSITMA CVVGYSDFK LPTELKWPLE RESLPVEPDL KPIMTQLKRQ TAGSADMPKF DDEYQAQARQ NQGTAPLNPY PGLTVTEPSF A NPAGGYAD ...String:
MIENKVELVA ELVLESIGKT EVVSRHTEGT KSCQVSFRIK DSPSEKGSTS FLSELVVIQT LDDNDKYTVV IRHGTSITMA CVVGYSDFK LPTELKWPLE RESLPVEPDL KPIMTQLKRQ TAGSADMPKF DDEYQAQARQ NQGTAPLNPY PGLTVTEPSF A NPAGGYAD GDLYPVGTSH PDWSGGLPNP LGNPSSQGGM IFDPNRRPAP RREDMPPGWM PGSKYDEPFG PGSGGFGGSG SG GFGGSGS GFI

UniProtKB: Silencing boundary-establishment protein FUB1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMTris(hydroxymethyl)aminomethaneTris
100.0 mMNaClsodium chloride
1.0 mMCH2N(CH2CO2H)2]2EDTA

Details: Sample was mixed with RvLEAMshort peptide to a final concentration of 1mg/ml sample and 30 micromolar RvLEAMshort immediately before preparation.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV
Details: wait time of 8 s, blot time of 12 s and a blot force of 8.
DetailsSample was mixed with RvLEAMshort peptide to a final concentration of 1mg/ml sample and 30 micromolar RvLEAMshort immediately before preparation.

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 11278 / Average exposure time: 6.32 sec. / Average electron dose: 50.253 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 2419467
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.14-c7) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: ab intio model
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0.1_cu12.2) / Number images used: 13428
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0.1_cu12.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0.1_cu12.2)
Final 3D classificationSoftware - Name: RELION (ver. 5.0.1_cu12.2)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: experimental model / Details: Model Angelo generated
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-10og:
20S Alpha 3 Deletion proteasome core particle in complex with Fub1 and Blm10

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more