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- EMDB-29764: Structure of the Plasmodium falciparum 20S proteasome complexed w... -

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Basic information

Entry
Database: EMDB / ID: EMD-29764
TitleStructure of the Plasmodium falciparum 20S proteasome complexed with inhibitor TDI-8304
Map data
Sample
  • Complex: Plasmodium falciparum 20S proteasome complexed with inhibitor TDI-8304
    • Protein or peptide: x 14 types
  • Ligand: x 2 types
Keywordsproteasome / inhibitor / 20S / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


proteasome core complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / proteasomal protein catabolic process / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / nucleus / cytoplasm
Similarity search - Function
Proteasome subunit alpha 1 / 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 subunit alpha 1 / 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
Proteasome subunit alpha type / Proteasome subunit alpha type-2 / Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit beta type-6 / Proteasome subunit alpha type-6 / Proteasome subunit alpha type-3 / Proteasome subunit beta ...Proteasome subunit alpha type / Proteasome subunit alpha type-2 / Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit beta type-6 / Proteasome subunit alpha type-6 / Proteasome subunit alpha type-3 / Proteasome subunit beta / Proteasome subunit alpha type-1 / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit alpha type
Similarity search - Component
Biological speciesPlasmodium falciparum NF54 (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.18 Å
AuthorsHsu H-C / Li H
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI143714 United States
CitationJournal: Nat Commun / Year: 2023
Title: Structures revealing mechanisms of resistance and collateral sensitivity of Plasmodium falciparum to proteasome inhibitors.
Authors: Hao-Chi Hsu / Daqiang Li / Wenhu Zhan / Jianxiang Ye / Yi Jing Liu / Annie Leung / Junling Qin / Benigno Crespo / Francisco-Javier Gamo / Hao Zhang / Liwang Cui / Alison Roth / Laura A ...Authors: Hao-Chi Hsu / Daqiang Li / Wenhu Zhan / Jianxiang Ye / Yi Jing Liu / Annie Leung / Junling Qin / Benigno Crespo / Francisco-Javier Gamo / Hao Zhang / Liwang Cui / Alison Roth / Laura A Kirkman / Huilin Li / Gang Lin /
Abstract: The proteasome of the malaria parasite Plasmodium falciparum (Pf20S) is an advantageous drug target because its inhibition kills P. falciparum in multiple stages of its life cycle and synergizes with ...The proteasome of the malaria parasite Plasmodium falciparum (Pf20S) is an advantageous drug target because its inhibition kills P. falciparum in multiple stages of its life cycle and synergizes with artemisinins. We recently developed a macrocyclic peptide, TDI-8304, that is highly selective for Pf20S over human proteasomes and is potent in vitro and in vivo against P. falciparum. A mutation in the Pf20S β6 subunit, A117D, confers resistance to TDI-8304, yet enhances both enzyme inhibition and anti-parasite activity of a tripeptide vinyl sulfone β2 inhibitor, WLW-vs. Here we present the high-resolution cryo-EM structures of Pf20S with TDI-8304, of human constitutive proteasome with TDI-8304, and of Pf20Sβ6 with WLW-vs that give insights into the species selectivity of TDI-8304, resistance to it, and the collateral sensitivity associated with resistance, including that TDI-8304 binds β2 and β5 in wild type Pf20S as well as WLW-vs binds β2 and β5 in Pf20Sβ6. We further show that TDI-8304 kills P. falciparum as quickly as chloroquine and artemisinin and is active against P. cynomolgi at the liver stage. This increases interest in using these structures to facilitate the development of Pf20S inhibitors that target multiple proteasome subunits and limit the emergence of resistance.
History
DepositionFeb 15, 2023-
Header (metadata) releaseDec 20, 2023-
Map releaseDec 20, 2023-
UpdateJan 3, 2024-
Current statusJan 3, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29764.png

Downloads & links

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Map

FileDownload / File: emd_29764.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.828 Å
Density
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.09359487 - 0.20018467
Average (Standard dev.)0.00025023715 (±0.00875001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 317.952 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_29764_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_29764_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_29764_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Plasmodium falciparum 20S proteasome complexed with inhibitor TDI-8304

EntireName: Plasmodium falciparum 20S proteasome complexed with inhibitor TDI-8304
Components
  • Complex: Plasmodium falciparum 20S proteasome complexed with inhibitor TDI-8304
    • Protein or peptide: Proteasome subunit alpha type-6
    • Protein or peptide: Proteasome subunit alpha type-2
    • Protein or peptide: Proteasome subunit alpha type
    • Protein or peptide: Proteasome subunit alpha type
    • Protein or peptide: Proteasome subunit alpha type
    • Protein or peptide: Proteasome subunit alpha type-1
    • Protein or peptide: Proteasome subunit alpha type-3
    • Protein or peptide: Proteasome subunit beta type-6
    • Protein or peptide: Proteasome subunit beta
    • Protein or peptide: Proteasome subunit beta
    • Protein or peptide: Proteasome subunit beta
    • Protein or peptide: Proteasome subunit beta
    • Protein or peptide: Proteasome subunit beta
    • Protein or peptide: Proteasome subunit beta
  • Ligand: (7S,10S,13S)-N-cyclopentyl-10-[2-(morpholin-4-yl)ethyl]-9,12-dioxo-13-(2-oxopyrrolidin-1-yl)-2-oxa-8,11-diazabicyclo[13.3.1]nonadeca-1(19),15,17-triene-7-carboxamide
  • Ligand: water

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Supramolecule #1: Plasmodium falciparum 20S proteasome complexed with inhibitor TDI-8304

SupramoleculeName: Plasmodium falciparum 20S proteasome complexed with inhibitor TDI-8304
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#14
Source (natural)Organism: Plasmodium falciparum NF54 (eukaryote)
Molecular weightTheoretical: 700 KDa

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Macromolecule #1: Proteasome subunit alpha type-6

MacromoleculeName: Proteasome subunit alpha type-6 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum NF54 (eukaryote)
Molecular weightTheoretical: 29.531656 KDa
SequenceString: MVRPSQSMYD RHLTIFSPDG NLYQIEYAIK AVKNTNITSV GVKGENCAVI ISQKKMATQY ISQDKLLDYN NITNIYNITD EIGCSMVGM PGDCLSMVYK ARSEASEFLY SNGYNVNAET LCRNICDKIQ VYTQHAYMRL HACSGMIIGI DENNKPELFK F DPSGFCAG ...String:
MVRPSQSMYD RHLTIFSPDG NLYQIEYAIK AVKNTNITSV GVKGENCAVI ISQKKMATQY ISQDKLLDYN NITNIYNITD EIGCSMVGM PGDCLSMVYK ARSEASEFLY SNGYNVNAET LCRNICDKIQ VYTQHAYMRL HACSGMIIGI DENNKPELFK F DPSGFCAG YRACVIGNKE QESISVLERL LEKRKKKIQQ ETIDEDIRNT TILAIEALQT ILAFDLKASE IEVAIVSTKN RN FTQISEK EIDNYLTYIA ERD

UniProtKB: Proteasome subunit alpha type-6

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Macromolecule #2: Proteasome subunit alpha type-2

MacromoleculeName: Proteasome subunit alpha type-2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum NF54 (eukaryote)
Molecular weightTheoretical: 26.556391 KDa
SequenceString: MADGEYSFSL TTFSPTGKLV QIEYALNRVS SSSPALGIRA KNGVIIATEK KSPNELIEEN SIFKIQQISE HIGIVYAGMP GDFRVLLKR ARKEAIRYSL QYGSEILVKE LVKIIASIVQ EFTQTGGVRP FGLSLLICGV DVYGYHLYQI DPSGCYFNWM A TCVGKDYQ ...String:
MADGEYSFSL TTFSPTGKLV QIEYALNRVS SSSPALGIRA KNGVIIATEK KSPNELIEEN SIFKIQQISE HIGIVYAGMP GDFRVLLKR ARKEAIRYSL QYGSEILVKE LVKIIASIVQ EFTQTGGVRP FGLSLLICGV DVYGYHLYQI DPSGCYFNWM A TCVGKDYQ NNMSFLEKRY NKDIEIEDAI HTAILTLKES YEGVLNEKNI EIGVAYDNKP FKILTQNEIK DYLIEIE

UniProtKB: Proteasome subunit alpha type-2

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Macromolecule #3: Proteasome subunit alpha type

MacromoleculeName: Proteasome subunit alpha type / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum NF54 (eukaryote)
Molecular weightTheoretical: 27.977664 KDa
SequenceString: MARRYDSRTT TFSPEGRLYQ VEYALEAINN ASITIGLITK DGVILGADKV FISKLIDKAN NYEKIYKIDK HIFCGVAGLN ADANILINQ SRLYAQRYLY NYNEVQPVSQ LVVQICDIKQ SYTQYGGLRP YGVSFLIGGY DTKDGYQLYH TDPSGNYSGW F ATAIGTNN ...String:
MARRYDSRTT TFSPEGRLYQ VEYALEAINN ASITIGLITK DGVILGADKV FISKLIDKAN NYEKIYKIDK HIFCGVAGLN ADANILINQ SRLYAQRYLY NYNEVQPVSQ LVVQICDIKQ SYTQYGGLRP YGVSFLIGGY DTKDGYQLYH TDPSGNYSGW F ATAIGTNN LTASSVLKQE WKNDMTLEEG LLLALKTLAK STDTEIPKSE KIELAYLTNK DGEVYQKYLT EKEIEELIKL YT QKYIKE

UniProtKB: Proteasome subunit alpha type

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Macromolecule #4: Proteasome subunit alpha type

MacromoleculeName: Proteasome subunit alpha type / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum NF54 (eukaryote)
Molecular weightTheoretical: 27.263285 KDa
SequenceString: MSYDRAITVF SPDGHLLQVE HALEAVKKGG CAVAIKSSNF AVLAVEKKNI PKLQNPKTTE KLIKLDEHNC LAFAGLNADA RVLVNKTRL ECQRYYLNMD EPAPVDYIAK YVAKVQQKFT HRGGVRPFGI ATLIAGFKNN KEICIYQTEP SGIYAAWKAQ A IGKNAKIV ...String:
MSYDRAITVF SPDGHLLQVE HALEAVKKGG CAVAIKSSNF AVLAVEKKNI PKLQNPKTTE KLIKLDEHNC LAFAGLNADA RVLVNKTRL ECQRYYLNMD EPAPVDYIAK YVAKVQQKFT HRGGVRPFGI ATLIAGFKNN KEICIYQTEP SGIYAAWKAQ A IGKNAKIV QEFLEKNYQE NMEQKDCIFL ALKAIFEVVE LSSKNVEVAL LTEKDLTFIE EQEINSMVEL IDQERTKNNE QN E

UniProtKB: Proteasome subunit alpha type

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Macromolecule #5: Proteasome subunit alpha type

MacromoleculeName: Proteasome subunit alpha type / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum NF54 (eukaryote)
Molecular weightTheoretical: 28.417367 KDa
SequenceString: MFSTRSEYDR GVNTFSPEGR LFQVEYALGA IKLGSTAVGI CVNDGVILAS ERRISSTLIE KDSVEKLLSI DDHIGCAMSG LMADARTLI DYARVECNHY KFIYNENINI KSCVELISEL ALDFSNLSDS KRKKIMSRPF GVALLIGGVD KNGPCLWYTE P SGTNTRFS ...String:
MFSTRSEYDR GVNTFSPEGR LFQVEYALGA IKLGSTAVGI CVNDGVILAS ERRISSTLIE KDSVEKLLSI DDHIGCAMSG LMADARTLI DYARVECNHY KFIYNENINI KSCVELISEL ALDFSNLSDS KRKKIMSRPF GVALLIGGVD KNGPCLWYTE P SGTNTRFS AASIGSAQEG AELLLQENYK KDMTFEQAEI LALTVLRQVM EDKLSTSNVE ICAIKKSDQT FYKYNTDDIS RI IDVLPSP VYPTIDMTA

UniProtKB: Proteasome subunit alpha type

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Macromolecule #6: Proteasome subunit alpha type-1

MacromoleculeName: Proteasome subunit alpha type-1 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum NF54 (eukaryote)
Molecular weightTheoretical: 28.742584 KDa
SequenceString: MYRNLYDTDN IIYSPEGRLY QVEYASEAIK QGTCAVAIKS KDYVVVSGLK KCISKLSFPQ EKIFKIDDYI GISMSGITSD AKVLTKFMQ NECLSHKFLY NENINIESLV RSVADKYQKN TQKSSKRAFG VGLMIAAYHN EPCIFETRPN GSYFEYDALS F GARSHASK ...String:
MYRNLYDTDN IIYSPEGRLY QVEYASEAIK QGTCAVAIKS KDYVVVSGLK KCISKLSFPQ EKIFKIDDYI GISMSGITSD AKVLTKFMQ NECLSHKFLY NENINIESLV RSVADKYQKN TQKSSKRAFG VGLMIAAYHN EPCIFETRPN GSYFEYDALS F GARSHASK TYLEKNLHLF EECSLEELIL HCLKALKCSL SSESELTISN TALAVVGKNH PWQEISSLQL EEYLSKVKMD AE QEQVEEN VQNEAN

UniProtKB: Proteasome subunit alpha type-1

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Macromolecule #7: Proteasome subunit alpha type-3

MacromoleculeName: Proteasome subunit alpha type-3 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum NF54 (eukaryote)
Molecular weightTheoretical: 29.324295 KDa
SequenceString: MAGLSAGYDL SVSTFSPDGR LYQVEYIYKS INNNNTALCL ECKDGIICCC INSNMDKNKM IKKNSYNRIY HVNNNIIITY SGFDGDARN IIDRARSEAN TYYYNFHTNI PLHILVNRIS LYIHAYTLYW HMRPFAASII ISSFNEKDKG DIYCIEPNGA C YKYSGIVI ...String:
MAGLSAGYDL SVSTFSPDGR LYQVEYIYKS INNNNTALCL ECKDGIICCC INSNMDKNKM IKKNSYNRIY HVNNNIIITY SGFDGDARN IIDRARSEAN TYYYNFHTNI PLHILVNRIS LYIHAYTLYW HMRPFAASII ISSFNEKDKG DIYCIEPNGA C YKYSGIVI GKNKEMFKTE IEKKDYKDIN VRDAIEDIYK FILTSDDHMN KNNLQNLVNF SWICKESSYE FQNIHEEILT PA LNKAVEY IEKLN

UniProtKB: Proteasome subunit alpha type-3

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Macromolecule #8: Proteasome subunit beta type-6

MacromoleculeName: Proteasome subunit beta type-6 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum NF54 (eukaryote)
Molecular weightTheoretical: 29.143936 KDa
SequenceString: TTIIGIIYDN GVMLACDSRT SSGTFISNKC SRKINRINEN LYVCRSGASA HSQKIIEIIK HYCVSMKNEN RKKGRFHEGE TIYDETTYD EEIDIDSINY LDYNNNNDNN LVTKNKYFYE DKFNDYNPLV ENVAHITKKI IYTNNNFLSC ALIFGGYDKI K KQQLYAVN ...String:
TTIIGIIYDN GVMLACDSRT SSGTFISNKC SRKINRINEN LYVCRSGASA HSQKIIEIIK HYCVSMKNEN RKKGRFHEGE TIYDETTYD EEIDIDSINY LDYNNNNDNN LVTKNKYFYE DKFNDYNPLV ENVAHITKKI IYTNNNFLSC ALIFGGYDKI K KQQLYAVN LNGSIIEKHD FAVSGSGSIY IQSYLQDKYK KFMTKKECFN LILNCVKYAM HNDNSSGGLI RIVNITKSFV EE FTVVNTQ MNFQY

UniProtKB: Proteasome subunit beta type-6

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Macromolecule #9: Proteasome subunit beta

MacromoleculeName: Proteasome subunit beta / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum NF54 (eukaryote)
Molecular weightTheoretical: 25.104885 KDa
SequenceString: TTICGLVCQN AVILGADTRA TEGPIVADKN CSKLHYISKN IWCAGAGVAG DLEHTTLWLQ HNVELHRLNT NTQPRVSMCV SRLTQELFK YQGYKVCAIV LGGVDVNGPQ LYGIHPHGSS CLLPFTALGS GSLNAMAVLE AKYRDNMTIE EGKNLVCEAI C AGIFNDLG ...String:
TTICGLVCQN AVILGADTRA TEGPIVADKN CSKLHYISKN IWCAGAGVAG DLEHTTLWLQ HNVELHRLNT NTQPRVSMCV SRLTQELFK YQGYKVCAIV LGGVDVNGPQ LYGIHPHGSS CLLPFTALGS GSLNAMAVLE AKYRDNMTIE EGKNLVCEAI C AGIFNDLG SGGNVDICVI TKDSYQHIRP YKEPNMRLYH LPHPTIYPKG TTPILSEKIE YIKKFISVED A

UniProtKB: Proteasome subunit beta

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Macromolecule #10: Proteasome subunit beta

MacromoleculeName: Proteasome subunit beta / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum NF54 (eukaryote)
Molecular weightTheoretical: 24.533131 KDa
SequenceString: MGSIYNYNGG CVLGMSGSNC VAIACDLRLG ANTFTTVSTK FSKIFKMNNN VYVGLSGLAT DIQTLYEILR YRVNLYEVRQ DAEMDVECF ANMLSSILYS NRFSPYFVNP IVVGFKLKHY VDEEGEKKVN YEPYLTAYDL IGAKCETRDF VVNGVTSEQL F GMCESLYV ...String:
MGSIYNYNGG CVLGMSGSNC VAIACDLRLG ANTFTTVSTK FSKIFKMNNN VYVGLSGLAT DIQTLYEILR YRVNLYEVRQ DAEMDVECF ANMLSSILYS NRFSPYFVNP IVVGFKLKHY VDEEGEKKVN YEPYLTAYDL IGAKCETRDF VVNGVTSEQL F GMCESLYV KDQDENGLFE TISQCLLSAL DRDCISGWGA EVLVLTPEKI IKKKLKARMD

UniProtKB: Proteasome subunit beta

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Macromolecule #11: Proteasome subunit beta

MacromoleculeName: Proteasome subunit beta / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum NF54 (eukaryote)
Molecular weightTheoretical: 22.889105 KDa
SequenceString: MDTLIGLRGN NFVVLAADTY SINSIIKLKN DDNTKFYDIH GNKCLLLGGS IGDRLQFGEF IRKNVHLYQY QNNTDMFVKS FAFFTRKNL AYYLRRNPFE VNCLIAGYDK KDGYQLYWCD YLSNMDSVNK GAHGYGAYLV SAILDKYYHE NLTVDEALDI F KLCFEELK ...String:
MDTLIGLRGN NFVVLAADTY SINSIIKLKN DDNTKFYDIH GNKCLLLGGS IGDRLQFGEF IRKNVHLYQY QNNTDMFVKS FAFFTRKNL AYYLRRNPFE VNCLIAGYDK KDGYQLYWCD YLSNMDSVNK GAHGYGAYLV SAILDKYYHE NLTVDEALDI F KLCFEELK KRFLLTQINY ELRIMYDNKV ETQYVTV

UniProtKB: Proteasome subunit beta

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Macromolecule #12: Proteasome subunit beta

MacromoleculeName: Proteasome subunit beta / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum NF54 (eukaryote)
Molecular weightTheoretical: 23.620646 KDa
SequenceString: TTTLAFKFKD GIIVAVDSRA SMGSFISSQN VEKIIEINKN ILGTMAGGAA DCLYWEKYLG KIIKIYELRN NEKISVRAAS TILSNILYQ YKGYGLCCGI ILSGYDHTGF NMFYVDDSGK KVEGNLFSCG SGSTYAYSIL DSAYDYNLNL DQAVELARNA I YHATFRDG ...String:
TTTLAFKFKD GIIVAVDSRA SMGSFISSQN VEKIIEINKN ILGTMAGGAA DCLYWEKYLG KIIKIYELRN NEKISVRAAS TILSNILYQ YKGYGLCCGI ILSGYDHTGF NMFYVDDSGK KVEGNLFSCG SGSTYAYSIL DSAYDYNLNL DQAVELARNA I YHATFRDG GSGGKVRVFH IHKNGYDKII EGEDVFDLHY HYTNPEQKDQ YVM

UniProtKB: Proteasome subunit beta

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Macromolecule #13: Proteasome subunit beta

MacromoleculeName: Proteasome subunit beta / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum NF54 (eukaryote)
Molecular weightTheoretical: 27.301203 KDa
SequenceString: MDLILYNDNL TEKKTEKENV IEHGRGFKRW YPYIDNGGTV IGLTGKDYVI LAADTRLSLS YSIYTRFCPK ISKLTDKCII GSSGMQSDI KTLHSLLQKK IQLFVLEHSH YPDIHVIARL LCVILYSRRF FPYYAFNILA GVDENNKGVL YNYDSVGSYC E ATHSCVGS ...String:
MDLILYNDNL TEKKTEKENV IEHGRGFKRW YPYIDNGGTV IGLTGKDYVI LAADTRLSLS YSIYTRFCPK ISKLTDKCII GSSGMQSDI KTLHSLLQKK IQLFVLEHSH YPDIHVIARL LCVILYSRRF FPYYAFNILA GVDENNKGVL YNYDSVGSYC E ATHSCVGS GSQLILPILD NRVEQKNQLI KNTNFNLGDD INFVKDAITS ATERDIYTGD KTLIYVIDKM GINVNTLDLK QD

UniProtKB: Proteasome subunit beta

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Macromolecule #14: Proteasome subunit beta

MacromoleculeName: Proteasome subunit beta / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum NF54 (eukaryote)
Molecular weightTheoretical: 30.909893 KDa
SequenceString: MTLGPVVTGT SVIAIKYKHG IMIAADRKAS YGSYAKFQNV ERIFKINNKT VMGFSGELAD AQYLHELLTR KNINNLSEKK RKEDMYTPQ HYHSYVSRVF YVRKNRIDPL FNNIIIAGIN SQKYDNNDDN VLLYTNKNND DEQNEYKNNE EYKEIHKDDL Y IGFVDMHG ...String:
MTLGPVVTGT SVIAIKYKHG IMIAADRKAS YGSYAKFQNV ERIFKINNKT VMGFSGELAD AQYLHELLTR KNINNLSEKK RKEDMYTPQ HYHSYVSRVF YVRKNRIDPL FNNIIIAGIN SQKYDNNDDN VLLYTNKNND DEQNEYKNNE EYKEIHKDDL Y IGFVDMHG TNFCDDYITT GYARYFALTL LRDHYKDNMT EEEARILINE CLRILYFRDA TSSNFIQIVK VTSKGVEYEE PY ILPCVLN SADYVYPSTL LPPAGCMW

UniProtKB: Proteasome subunit beta

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Macromolecule #15: (7S,10S,13S)-N-cyclopentyl-10-[2-(morpholin-4-yl)ethyl]-9,12-diox...

MacromoleculeName: (7S,10S,13S)-N-cyclopentyl-10-[2-(morpholin-4-yl)ethyl]-9,12-dioxo-13-(2-oxopyrrolidin-1-yl)-2-oxa-8,11-diazabicyclo[13.3.1]nonadeca-1(19),15,17-triene-7-carboxamide
type: ligand / ID: 15 / Number of copies: 6 / Formula: YRE
Molecular weightTheoretical: 597.745 Da
Chemical component information

ChemComp-YRE:
(7S,10S,13S)-N-cyclopentyl-10-[2-(morpholin-4-yl)ethyl]-9,12-dioxo-13-(2-oxopyrrolidin-1-yl)-2-oxa-8,11-diazabicyclo[13.3.1]nonadeca-1(19),15,17-triene-7-carboxamide

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Macromolecule #16: water

MacromoleculeName: water / type: ligand / ID: 16 / Number of copies: 218 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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

Concentration0.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMTris
100.0 mMKClKCl
5.0 mMMgCl2MgCl2
1.0 mMDTT
2.0 %DMF
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 11520 pixel / Digitization - Dimensions - Height: 8184 pixel / Number grids imaged: 1 / Number real images: 29343 / Average exposure time: 1.5 sec. / Average electron dose: 66.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 657066
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 2.8)
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.18 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 305581
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6muw


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 21.44
Output model

PDB-8g6e:
Structure of the Plasmodium falciparum 20S proteasome complexed with inhibitor TDI-8304

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