[English] 日本語
Yorodumi
- EMDB-19523: Proteasomal late precursor complex from pre1-1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-19523
TitleProteasomal late precursor complex from pre1-1
Map data
Sample
  • Complex: Proteasomal late precursor complex from pre1-1
    • Protein or peptide: x 17 types
  • Ligand: x 1 types
Keywordsproteasome biogenesis / Ump1 / pre1-1 / cryo-EM / propertied maturation / HYDROLASE
Function / homology
Function and homology information


regulation of proteasome core complex assembly / proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 ...regulation of proteasome core complex assembly / proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / Ub-specific processing proteases / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / Neutrophil degranulation / proteasome complex / peroxisome / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / mRNA binding / DNA damage response / endoplasmic reticulum membrane / mitochondrion / nucleus / cytosol / cytoplasm
Similarity search - Function
Proteasome chaperone 1, fungi / Proteasome chaperone 1 superfamily / POC1 chaperone / Proteasome maturation factor Ump1 / Proteasome maturation factor UMP1 / Proteasome assembly chaperone 2, eukaryotic / Proteasome assembly chaperone 2 / Proteasome assembly chaperone 2 superfamily / PAC2 family / Proteasome beta subunit, C-terminal ...Proteasome chaperone 1, fungi / Proteasome chaperone 1 superfamily / POC1 chaperone / Proteasome maturation factor Ump1 / Proteasome maturation factor UMP1 / Proteasome assembly chaperone 2, eukaryotic / Proteasome assembly chaperone 2 / Proteasome assembly chaperone 2 superfamily / PAC2 family / 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
Probable proteasome subunit alpha type-7 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-6 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 / 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-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-6 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 / Proteasome subunit beta type-5 / Proteasome subunit beta type-7 / Proteasome subunit alpha type-5 / Proteasome assembly chaperone 2 / Proteasome maturation factor UMP1 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-6 / Proteasome subunit alpha type-4 / Proteasome chaperone 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.14 Å
AuthorsMark E / Ramos PC / Kayser F / Hoeckendorff J / Dohmen RJ / Wendler P
Funding support Germany, European Union, 3 items
OrganizationGrant numberCountry
German Research Foundation (DFG)406260942 Germany
German Research Foundation (DFG)442219341 Germany
iNEXT23209European Union
CitationJournal: Life Sci Alliance / Year: 2024
Title: Structural roles of Ump1 and β-subunit propeptides in proteasome biogenesis.
Authors: Eric Mark / Paula C Ramos / Fleur Kayser / Jörg Höckendorff / R Jürgen Dohmen / Petra Wendler /
Abstract: The yeast (β4-S142F) mutant accumulates late 20S proteasome core particle precursor complexes (late-PCs). We report a 2.1 Å cryo-EM structure of this intermediate with full-length Ump1 trapped ...The yeast (β4-S142F) mutant accumulates late 20S proteasome core particle precursor complexes (late-PCs). We report a 2.1 Å cryo-EM structure of this intermediate with full-length Ump1 trapped inside, and Pba1-Pba2 attached to the α-ring surfaces. The structure discloses intimate interactions of Ump1 with β2- and β5-propeptides, which together fill most of the antechambers between the α- and β-rings. The β5-propeptide is unprocessed and separates Ump1 from β6 and β7. The β2-propeptide is disconnected from the subunit by autocatalytic processing and localizes between Ump1 and β3. A comparison of different proteasome maturation states reveals that maturation goes along with global conformational changes in the rings, initiated by structuring of the proteolytic sites and their autocatalytic activation. In the strain, β2 is activated first enabling processing of β1-, β6-, and β7-propeptides. Subsequent maturation of β5 and β1 precedes degradation of Ump1, tightening of the complex, and finally release of Pba1-Pba2.
History
DepositionFeb 1, 2024-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateSep 25, 2024-
Current statusSep 25, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_19523.png

Downloads & links

-
Map

FileDownload / File: emd_19523.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 600 pix.
= 500.4 Å		0.83 Å/pix.
x 600 pix.
= 500.4 Å		0.83 Å/pix.
x 600 pix.
= 500.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.282
Minimum - Maximum-1.4400984 - 2.189207
Average (Standard dev.)-0.00017070438 (±0.051281784)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 500.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_19523_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_19523_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_19523_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Proteasomal late precursor complex from pre1-1

EntireName: Proteasomal late precursor complex from pre1-1
Components
  • Complex: Proteasomal late precursor complex from pre1-1
    • Protein or peptide: Proteasome subunit beta type-6
    • Protein or peptide: Proteasome subunit beta type-7
    • Protein or peptide: Proteasome maturation factor UMP1
    • Protein or peptide: Proteasome chaperone 1
    • Protein or peptide: Proteasome assembly chaperone 2
    • Protein or peptide: Proteasome subunit alpha type-1
    • Protein or peptide: Proteasome subunit alpha type-2
    • Protein or peptide: Proteasome subunit alpha type-3
    • Protein or peptide: Proteasome subunit alpha type-4
    • Protein or peptide: Proteasome subunit alpha type-5
    • Protein or peptide: Proteasome subunit alpha type-6
    • Protein or peptide: Probable 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
  • Ligand: water

+
Supramolecule #1: Proteasomal late precursor complex from pre1-1

SupramoleculeName: Proteasomal late precursor complex from pre1-1 / type: complex / ID: 1 / Parent: 0
Macromolecule list: #7, #1, #8-#10, #2, #11-#12, #3-#5, #13, #6, #14-#17
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

+
Macromolecule #1: Proteasome subunit beta type-7

MacromoleculeName: Proteasome subunit beta type-7 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's 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 #2: Proteasome subunit alpha type-1

MacromoleculeName: Proteasome subunit alpha type-1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's 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 #3: Proteasome subunit alpha type-4

MacromoleculeName: Proteasome subunit alpha type-4 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's 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 #4: Proteasome subunit alpha type-5

MacromoleculeName: Proteasome subunit alpha type-5 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's 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 #5: Proteasome subunit alpha type-6

MacromoleculeName: Proteasome subunit alpha type-6 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's 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 #6: Proteasome subunit beta type-1

MacromoleculeName: Proteasome subunit beta type-1 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Saccharomyces cerevisiae (brewer's 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 #7: Proteasome subunit beta type-6

MacromoleculeName: Proteasome subunit beta type-6 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's 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 #8: Proteasome maturation factor UMP1

MacromoleculeName: Proteasome maturation factor UMP1 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 16.777766 KDa
SequenceString:
MNIVPQDTFK SQVSTDQDKS VLSSAVPSLP DTLRQQEGGA VPLSTQLNDR HPLESTLKNW ETTQRQRQME QYRQIFGIAE PMKRTMEME IVNRTDFNPL STNGSIHRDI LLNKECSIDW EDVYPGTGLQ ASTMVGDDVH SKIEKQLGI

UniProtKB: Proteasome maturation factor UMP1

+
Macromolecule #9: Proteasome chaperone 1

MacromoleculeName: Proteasome chaperone 1 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 30.718074 KDa
SequenceString: MLFKQWNDLP EPKHLLDLPE ISKNLQSLEV CPVPKVEFPQ DLDVPQYSTA VITTKIMNPL FPKNLLQLTS IGEIKTTLTV KSPSLPQSS GKHSWNYDEN FPNEVDPDQK NDTADETVYG FSFPIYSFGK TLLFSMEENF ISISPIFGNM ISRSIISQLA Q FSPDIIVI ...String:
MLFKQWNDLP EPKHLLDLPE ISKNLQSLEV CPVPKVEFPQ DLDVPQYSTA VITTKIMNPL FPKNLLQLTS IGEIKTTLTV KSPSLPQSS GKHSWNYDEN FPNEVDPDQK NDTADETVYG FSFPIYSFGK TLLFSMEENF ISISPIFGNM ISRSIISQLA Q FSPDIIVI GTSDKIASMK VMTENECTLQ PPEFITGFIG SVLTQLIVGP SKGLKFKCLV APSEGPNGFE KLSLSDMGSL VD LCGQWLG FEPSRYSEEC YRLWRCDSAA IGAQSGLYI

UniProtKB: Proteasome chaperone 1

+
Macromolecule #10: Proteasome assembly chaperone 2

MacromoleculeName: Proteasome assembly chaperone 2 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 30.762895 KDa
SequenceString: MSCLVLPLVS VGNIPQLSID WLLNSQANEW EYLEALDSKY LVEFVGPLDR PEDGSDSLYK DADMKYSSAL EVFYNKKRGL FAIQQRTPL VSVNYLNNFI VEIILPFLSK YNISEICIWD SLYAMEDENG VIVRPQEVYS LGEFYFDDEA ELLSNLHLND Q ESMVNNWL ...String:
MSCLVLPLVS VGNIPQLSID WLLNSQANEW EYLEALDSKY LVEFVGPLDR PEDGSDSLYK DADMKYSSAL EVFYNKKRGL FAIQQRTPL VSVNYLNNFI VEIILPFLSK YNISEICIWD SLYAMEDENG VIVRPQEVYS LGEFYFDDEA ELLSNLHLND Q ESMVNNWL HFTPTSFQDK ISVDQPIFKI LFQILNASQR PKALRSIKYC SCLANEGDNS LDSQQFLQWI ISQKVIKNAP PI VKFVRPI SWQGAYGMAD ARDKFVDLYN

UniProtKB: Proteasome assembly chaperone 2

+
Macromolecule #11: Proteasome subunit alpha type-2

MacromoleculeName: Proteasome subunit alpha type-2 / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's 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 #12: Proteasome subunit alpha type-3

MacromoleculeName: Proteasome subunit alpha type-3 / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 28.74823 KDa
SequenceString: MGSRRYDSRT TIFSPEGRLY QVEYALESIS HAGTAIGIMA SDGIVLAAER KVTSTLLEQD TSTEKLYKLN DKIAVAVAGL TADAEILIN TARIHAQNYL KTYNEDIPVE ILVRRLSDIK QGYTQHGGLR PFGVSFIYAG YDDRYGYQLY TSNPSGNYTG W KAISVGAN ...String:
MGSRRYDSRT TIFSPEGRLY QVEYALESIS HAGTAIGIMA SDGIVLAAER KVTSTLLEQD TSTEKLYKLN DKIAVAVAGL TADAEILIN TARIHAQNYL KTYNEDIPVE ILVRRLSDIK QGYTQHGGLR PFGVSFIYAG YDDRYGYQLY TSNPSGNYTG W KAISVGAN TSAAQTLLQM DYKDDMKVDD AIELALKTLS KTTDSSALTY DRLEFATIRK GANDGEVYQK IFKPQEIKDI LV KTGITKK DEDEEADEDM K

UniProtKB: Proteasome subunit alpha type-3

+
Macromolecule #13: Probable proteasome subunit alpha type-7

MacromoleculeName: Probable proteasome subunit alpha type-7 / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's 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 #14: Proteasome subunit beta type-2

MacromoleculeName: Proteasome subunit beta type-2 / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Saccharomyces cerevisiae (brewer's 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 #15: Proteasome subunit beta type-3

MacromoleculeName: Proteasome subunit beta type-3 / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's 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 #16: Proteasome subunit beta type-4

MacromoleculeName: Proteasome subunit beta type-4 / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 24.431629 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MDIILGIRVQ DSVILASSKA VTRGISVLKD SDDKTRQLSP HTLMSFAGEA GDTVQFAEYI QANIQLYSIR EDYELSPQAV SSFVRQELA KSIRSRRPYQ VNVLIGGYDK KKNKPELYQI DYLGTKVELP YGAHGYSGFY TFFLLDHHYR PDMTTEEGLD L LKLCVQEL ...String:
MDIILGIRVQ DSVILASSKA VTRGISVLKD SDDKTRQLSP HTLMSFAGEA GDTVQFAEYI QANIQLYSIR EDYELSPQAV SSFVRQELA KSIRSRRPYQ VNVLIGGYDK KKNKPELYQI DYLGTKVELP YGAHGYSGFY TFFLLDHHYR PDMTTEEGLD L LKLCVQEL EKRMPMDFKG VIVKIVDKDG IRQVDDFQAQ DYKDDDDKHH HHHH

UniProtKB: Proteasome subunit beta type-4

+
Macromolecule #17: Proteasome subunit beta type-5

MacromoleculeName: Proteasome subunit beta type-5 / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Saccharomyces cerevisiae (brewer's 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 #18: water

MacromoleculeName: water / type: ligand / ID: 18 / Number of copies: 2790 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.35 mg/mL
BufferpH: 7.5 / Details: 150 mM NaCl 50 mM Tris-HCl
GridModel: Quantifoil R2/4 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.02 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER
Details: manual plunge freezing device purchased from 'Neptune Fluid Flow Systems'.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 29904 / Average exposure time: 2.0 sec. / Average electron dose: 44.0 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: 1.8 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 10556408
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.14 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3) / Number images used: 233748
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3)
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. 4.3)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8rvl:
Proteasomal late precursor complex from pre1-1

+
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://pdbjlvh1.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