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- EMDB-46570: Core particle assembly intermediate Capless 13S purified from Sac... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-46570
TitleCore particle assembly intermediate Capless 13S purified from Saccharomyces cerevisiae
Map data
Sample
  • Complex: Proteasome assembly intermediate
    • Protein or peptide: x 11 types
KeywordsProteasome / Cryo-EM / Assembly / assembly chaperone / Blm10 / PA200 / Blm10-13S / Pba1 / CP / HYDROLASE
Function / homology
Function and homology information


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 / 3-deoxy-7-phosphoheptulonate synthase ...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 / 3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / Neddylation / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / chorismate biosynthetic process / Ub-specific processing proteases / proteasome endopeptidase complex / endopeptidase activator activity / proteasome core complex, beta-subunit complex / proteasome assembly / aromatic amino acid family biosynthetic process / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / amino acid biosynthetic process / Neutrophil degranulation / proteasome complex / ubiquitin-dependent protein catabolic process / endopeptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA damage response / endoplasmic reticulum membrane / mitochondrion / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Proteasome maturation factor Ump1 / Proteasome maturation factor UMP1 / DAHP synthetase, class II / Class-II DAHP synthetase family / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha5 / Proteasome subunit alpha6 ...Proteasome maturation factor Ump1 / Proteasome maturation factor UMP1 / DAHP synthetase, class II / Class-II DAHP synthetase family / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / 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 / Aldolase-type TIM barrel
Similarity search - Domain/homology
Phospho-2-dehydro-3-deoxyheptonate aldolase / 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
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.55 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: To Be Published
Title: Structure of Blm10:13S proteasome assembly intermediate reveals parallel assembly pathways for the proteasome core particle
Authors: Kaur M / Chen X / Lee SY / Weaver TM / Freudenthal BD / Walters KJ / Roelofs J
History
DepositionAug 13, 2024-
Header (metadata) releaseAug 20, 2025-
Map releaseAug 20, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: RCSB / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_46570.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.068 Å
Density
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-0.057544064 - 12.256069
Average (Standard dev.)0.008743938 (±0.34902874)
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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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 maturation factor UMP1

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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: 288 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: Phospho-2-dehydro-3-deoxyheptonate aldolase

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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 maturation factor UMP1

MacromoleculeName: Proteasome maturation factor UMP1 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
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

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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

Concentration1.80 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMC4H12NO3ClTris(hydroxymethyl)aminomethane hydrochloride
5.0 mMMgCl2Magnesium dichloride
2.0 mMC14H24N2O10EGTA
1.0 mMC14H9Cl5Dichlorodiphenyltrichloroethane
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

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 5235 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 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
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 108417
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.4.1)

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Atomic model buiding 1

Initial model
PDB IDChain

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: 128.66 / Target criteria: Cross-correlation coefficient
Output model

PDB-9d4u:
Core particle assembly intermediate Capless 13S purified from Saccharomyces cerevisiae

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