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- EMDB-46461: Core particle assembly intermediate 1 purified from Saccharomyces... -

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Basic information

Entry
Database: EMDB / ID: EMD-46461
TitleCore particle assembly intermediate 1 purified from Saccharomyces cerevisiae
Map data
Sample
  • Complex: Proteasome assembly intermediate
    • Protein or peptide: x 12 types
KeywordsProteasome / assembly chaperone / Blm10 / PA200 / Blm10-13S / Pba1 / CP / HYDROLASE
Function / homology
Function and homology information


proteasome core complex import into nucleus / : / myosin-light-chain kinase / myosin light chain kinase activity / myosin light chain binding / proteasome storage granule assembly / peptidase activator activity / cardiac muscle tissue morphogenesis / proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network ...proteasome core complex import into nucleus / : / myosin-light-chain kinase / myosin light chain kinase activity / myosin light chain binding / proteasome storage granule assembly / peptidase activator activity / cardiac muscle tissue morphogenesis / proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Proteasome assembly / 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 / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / Neddylation / proteasome binding / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / endopeptidase activator activity / Ub-specific processing proteases / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome assembly / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / striated muscle contraction / regulation of proteasomal protein catabolic process / Neutrophil degranulation / proteasome complex / : / ubiquitin-dependent protein catabolic process / endopeptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / calmodulin binding / DNA repair / mRNA binding / DNA damage response / endoplasmic reticulum membrane / signal transduction / mitochondrion / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Proteasome activator Blm10, N-terminal / Proteasome-substrate-size regulator, N-terminal / Myosin light chain kinase 2, catalytic domain / 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 activator Blm10, N-terminal / Proteasome-substrate-size regulator, N-terminal / Myosin light chain kinase 2, catalytic domain / 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 maturation factor Ump1 / Proteasome maturation factor UMP1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / 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 / Armadillo-type fold / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Myosin light chain kinase 2, skeletal/cardiac muscle / 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-2 / Proteasome subunit beta type-3 / Proteasome subunit alpha type-5 / Proteasome maturation factor UMP1 ...Myosin light chain kinase 2, skeletal/cardiac muscle / 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-2 / Proteasome subunit beta type-3 / Proteasome subunit alpha type-5 / Proteasome maturation factor UMP1 / Proteasome subunit alpha type-6 / Proteasome subunit alpha type-4 / Proteasome activator BLM10
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsChen X / Kaur M / Roelofs J / Walters KJ
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1 ZIA BC011490 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM149314 United States
CitationJournal: bioRxiv / Year: 2024
Title: Structure of Blm10:13S proteasome intermediate reveals parallel assembly pathways for the proteasome core particle.
Authors: Mandeep Kaur / Xiang Chen / Stella Y Lee / Tyler M Weaver / Bret D Freudenthal / Kylie J Walters / Jeroen Roelofs /
Abstract: Proteasomes are formed by chaperone-assisted assembly of core particles (CPs) and regulatory particles (RPs). The CP chaperone dimer Pba1/Pba2 binds early to proteasome subunits, and is thought to be ...Proteasomes are formed by chaperone-assisted assembly of core particles (CPs) and regulatory particles (RPs). The CP chaperone dimer Pba1/Pba2 binds early to proteasome subunits, and is thought to be replaced by Blm10 to form Blm10:CP, which promotes ATP-independent degradation of disordered proteins. Here, we present evidence of distinct parallel assembly pathways for CP by solving five cryo-EM structures including a Blm10:13S pre-assembly intermediate. Our data conflict with the current model of Blm10 and Pba1/Pba2 sequential activity in a single assembly pathway, as we find their CP binding is mutually exclusive and both are present on early and late assembly intermediates. CP affinity for Pba1/Pba2 is reduced during maturation, promoting Pba1/Pba2 release. We find Blm10 undergoes no such affinity switch, suggesting this pathway predominantly yields mature Blm10-bound CP. Altogether, our findings conflict with the current paradigm of sequential CP binding to instead indicate parallel assembly pathways by Pba1/Pba2 and Blm10.
History
DepositionAug 7, 2024-
Header (metadata) releaseDec 4, 2024-
Map releaseDec 4, 2024-
UpdateDec 4, 2024-
Current statusDec 4, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46461.png

Downloads & links

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Map

FileDownload / File: emd_46461.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 340 pix.
= 363.12 Å		1.07 Å/pix.
x 340 pix.
= 363.12 Å		1.07 Å/pix.
x 340 pix.
= 363.12 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-0.48313555 - 23.595661
Average (Standard dev.)0.028083785 (±0.6040232)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 363.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_46461_msk_1.map
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Half map: #2

Fileemd_46461_half_map_1.map
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Half map: #1

Fileemd_46461_half_map_2.map
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Sample components

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Entire : Proteasome assembly intermediate

EntireName: Proteasome assembly intermediate
Components
  • Complex: Proteasome assembly intermediate
    • 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-2
    • Protein or peptide: Proteasome subunit beta type-3
    • Protein or peptide: Proteasome subunit beta type-4
    • Protein or peptide: Proteasome activator BLM10
    • Protein or peptide: Proteasome maturation factor UMP1,Myosin light chain kinase 2, skeletal/cardiac muscle

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Supramolecule #1: Proteasome assembly intermediate

SupramoleculeName: Proteasome assembly intermediate / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 534 KDa

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Macromolecule #1: Proteasome subunit alpha type-1

MacromoleculeName: Proteasome subunit alpha type-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 28.03383 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
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

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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: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 27.191828 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
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

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Macromolecule #3: Proteasome subunit alpha type-3

MacromoleculeName: Proteasome subunit alpha type-3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 28.74823 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
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

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Macromolecule #4: Proteasome subunit alpha type-4

MacromoleculeName: Proteasome subunit alpha type-4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 28.478111 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
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

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Macromolecule #5: Proteasome subunit alpha type-5

MacromoleculeName: Proteasome subunit alpha type-5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 28.649086 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
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

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Macromolecule #6: Proteasome subunit alpha type-6

MacromoleculeName: Proteasome subunit alpha type-6 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 25.634 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
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

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Macromolecule #7: Probable proteasome subunit alpha type-7

MacromoleculeName: Probable proteasome subunit alpha type-7 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 31.575068 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
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

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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: 1 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 28.299889 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
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

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Macromolecule #9: Proteasome subunit beta type-3

MacromoleculeName: Proteasome subunit beta type-3 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 22.627842 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
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

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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: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 22.545676 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
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

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Macromolecule #11: Proteasome activator BLM10

MacromoleculeName: Proteasome activator BLM10 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 246.282375 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MTANNDDDIK SPIPITNKTL SQLKRFERSP GRPSSSQGEI KRKKSRLYAA DGRPHSPLRA RSATPTLQDQ KLFNGMDSTS LLNERLQHY TLDYVSDRAQ HMKNIYDPSS RWFSRSVRPE FPIEEFLPYK TESHEDQAKY LCHVLVNLYI AISSLDIQGL I SISSKDLA ...String:
MTANNDDDIK SPIPITNKTL SQLKRFERSP GRPSSSQGEI KRKKSRLYAA DGRPHSPLRA RSATPTLQDQ KLFNGMDSTS LLNERLQHY TLDYVSDRAQ HMKNIYDPSS RWFSRSVRPE FPIEEFLPYK TESHEDQAKY LCHVLVNLYI AISSLDIQGL I SISSKDLA DLKKEVDDLA LKTDLFRLSN NTAENDLLGN DIADYDDAEG LEDELDEYFD LAGPDFNATG KITAKSATIV NV NHWTNEL KNCLHFDFPV ALRKSLATVY YYLSLVQGQK VYRQMHVDMF ERLVSLDDDR TNFTELLQKQ GLLLDHQIML NFL CEFLPY PDPDYARYEL SSKEDLQLFR LLLKHAHNAK PFFDKSKESL LVDTMNFLLS SLAPSTMMAV MPIVTSVVPY HYHI HSKII DYFPFCYSIW SSVSANVAID THMYDFVGSI SKDVHNKILS SEHEKDVVGV EFGEFGIFTD DQMTFMFNRL QGHLR TDGQ IHSYSRTVKP FVYAINGSKK DRFFEKLVSL AKAIETFIHP SNNGFWTKPN AKFVHAFIKS YHGRVKYEED ICARGV TNG ICLTSFCHEE IVEIFLNIIS LGSQNKNPDI ANYYISCFAY LLELDPSNAY LIYDKILIDL YDTLADQFIN SRHRIIS SL KQFTRVIRFI VMDKLYRVHI TNVLSMLVSK LDMNDTNLTS NLINGIVSIA AFIPIQDLTG EDDYISFESD TLPLVQQH F YHIKCGESSK TFRVDDELLN NAFKASTTVF QSMLKVYVEK IFQLVDVDLE DSLVTKINQT TMILQESMDD KIFNYFASL LQRNFWSNDS FKEKDPNYEL VTIPLAALVR RNNGLSKELV RTLLFHIKEQ IKRGAGSVRS TSEIQQRDVK LVLYLTALND VLRQCHESL LEYSDELITF MKYLYDNVTN PPLDVITSIV IHSALATLCT TEITDCRLFP EDSKIPEKDR WGGLQFDPRR F DKQHLSFQ WHVPSSDEIT LSISILESLS EYCINNVEEL MKAPRHDSEY GDMIQKYVLV MTHTLSGSSL LFDPDFNKYR TQ SNLSYRE KLILLKNIRE NNCDPQELDI DIEQIRSGKD DEDYIESKDI EAGLNAGVSD VVQLRDEFPD ELIVDEEVVS EMP SGVNTP IAGTHGTDNS AMSSDLAFRD LDIYTCNYYF GNTTEEKLQN PQYLQVHRVR ARIGHFFHKL YVFLSTNFEN NTNM FQILL HGLKVWFTDL GQETVFNEDP NAFIDVDFLE NVQSLSHVNE PFTRTNFAIR ANSLHQSRVL LHSTNRKASK LENLL LVDI IQLATSLYPD IYKPAQGTLV HCMKQLVGSY GVVINKIIPS LEKAIKDHDY MKIQVILNVL LIKKIHRKLM TDYKDI GRL IFLLIECCRV NELEIGMYAD KILTDIVIGI KIPSSVCVIS DQAFLPLAPP DGTINLQVEA VKLAKKKKRE YYLSLLV DL QDKLLDKLDN EKDMGWKIRM FILRFVTQIQ SNLESKPDKR AVFSIISQIS TKHPEIIHLV VKSLLSTCNK IISLSDYE Y DITRAYKNEF NPSFVEILDT STTSFPKTFT EEMNNFDNPK YFIDLRAYVG WLCWGRLMYV MSPKALKLNL RENELEVLK TAGHLLTREF LRDVTMNLVQ DNETRGVFSS GNVSFFSLVI LLISSGFCEL NMSDLFELCE SYYNKDDKAS MIMSVEIVAG LVCGSKFMS VSDLDKRDTF IENFLAKCLD YELNHDAFEI WSTLAWWLPA VVDLRRSKTF FCHFINADGM FDRESDAATH Q TSKIYMLR SILMSMEFRA PDVGKLFDEL VFDHPYDQVR QAVAKLLTTL VQNQSNPSIS DPTTLLEAER NDPDGLGLPL KS VPEKVDA YIKKQFEIIK NLEDSVVGLN PQQFIKTDYF YRTSTIFYWI KEMARGPNKV LLVPYLVDYV LPFLIGLVKH KDV CALASL DPVRLYAGLG YMPIRKNHVA AIVDYVCSSN VALSSNQTKL QLAFIQHFLS AELLQLTEEE KNKILEFVVS NLYN EQFVE VRVRAASILS DIVHNWKEEQ PLLSLIERFA KGLDVNKYTS KERQKLSKTD IKIHGNVLGL GAIISAFPYV FPLPP WIPK QLSNLSSWAR TSGMTGQAAK NTISEFKKVR ADTWKFDRAS FNTEELEDLE GVLWRSYYA

UniProtKB: Proteasome activator BLM10

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Macromolecule #12: Proteasome maturation factor UMP1,Myosin light chain kinase 2, sk...

MacromoleculeName: Proteasome maturation factor UMP1,Myosin light chain kinase 2, skeletal/cardiac muscle
type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO / EC number: myosin-light-chain kinase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 22.753646 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MNIVPQDTFK SQVSTDQDKS VLSSAVPSLP DTLRQQEGGA VPLSTQLNDR HPLESTLKNW ETTQRQRQME QYRQIFGIAE PMKRTMEME IVNRTDFNPL STNGSIHRDI LLNKECSIDW EDVYPGTGLQ ASTMVGDDVH SKIEKQLGIG RRIPGLINPW K RRWKKNFI ...String:
MNIVPQDTFK SQVSTDQDKS VLSSAVPSLP DTLRQQEGGA VPLSTQLNDR HPLESTLKNW ETTQRQRQME QYRQIFGIAE PMKRTMEME IVNRTDFNPL STNGSIHRDI LLNKECSIDW EDVYPGTGLQ ASTMVGDDVH SKIEKQLGIG RRIPGLINPW K RRWKKNFI AVSAANRFKK ISSSGALDYD IPTTASENLY FQ

UniProtKB: Proteasome maturation factor UMP1, Myosin light chain kinase 2, skeletal/cardiac muscle

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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

Concentration1.8 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMC4H12NO3ClTris(hydroxymethyl)aminomethane hydrochloride
5.0 mMMgCl2Magnesium dichloride
2.0 mMC14H24N2O10EGTA
1.0 mMC14H9Cl5Dichlorodiphenyltrichloroethane

Details: 50 mM Tris-HCl, pH 7.5, 5 mM MgCl2, 2 mM EGTA, 1 mM DDT
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.042 kPa / Details: 0.42 mBar, 15mA
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 298.15 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 58 / Average electron dose: 1.034 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: 0.9 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4058518
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 586158
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.4.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

4v7o

chain_id: CA, source_name: PDB, initial_model_type: experimental model

4v7o

chain_id: DA, source_name: PDB, initial_model_type: experimental model

4v7o

chain_id: EA, source_name: PDB, initial_model_type: experimental model

7lsx

chain_id: A, source_name: PDB, initial_model_type: experimental model

7lsx

chain_id: B, source_name: PDB, initial_model_type: experimental model

7lsx

chain_id: C, source_name: PDB, initial_model_type: experimental model

7lsx

chain_id: D, source_name: PDB, initial_model_type: experimental model

7lsx

chain_id: E, source_name: PDB, initial_model_type: experimental model

7lsx

chain_id: F, source_name: PDB, initial_model_type: experimental model

7lsx

chain_id: G, source_name: PDB, initial_model_type: experimental model

7lsx

chain_id: H, source_name: PDB, initial_model_type: experimental model

7lsx

chain_id: I, source_name: PDB, initial_model_type: experimental model

7lsx

chain_id: J, source_name: PDB, initial_model_type: experimental model

7lsx

chain_id: K, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 120.13 / Target criteria: Cross-correlation coefficient
Output model

PDB-9d0t:
Core particle assembly intermediate 1 purified from Saccharomyces cerevisiae

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