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- EMDB-72277: Cryo-EM map of Plasmodium falciparum 20S proteasome bound to an a... -

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Basic information

Entry
Database: EMDB / ID: EMD-72277
TitleCryo-EM map of Plasmodium falciparum 20S proteasome bound to an asparagine-ethylenediamine based inhibitor TDI6245
Map data
Sample
  • Complex: Complex of Plasmodium falciparum 20S with inhibitor TDI-6245
    • Protein or peptide: x 14 types
  • Ligand: x 1 types
KeywordsPlasmodium falciparum antimalarial proteasome inhibitors / HYDROLASE
Function / homology
Function and homology information


proteasome core complex / : / proteasome core complex, beta-subunit complex / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / peptidase activity / 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 alpha5 / Proteasome subunit alpha6 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site ...Proteasome subunit alpha 1 / : / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha5 / Proteasome subunit alpha6 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal
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 / Uncharacterized protein / Proteasome alpha-type subunits domain-containing protein / Proteasome alpha-type subunits domain-containing protein / 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 / Uncharacterized protein / Proteasome alpha-type subunits domain-containing protein / Proteasome alpha-type subunits domain-containing protein / Proteasome subunit beta / Proteasome alpha-type subunits domain-containing protein / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit alpha type
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsHsu HC / Li H
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI123794 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI143714 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI177635 United States
CitationJournal: ACS Omega / Year: 2026
Title: Structure-Activity Relationship Study of Antimalarial Asparagine-Derived Proteasome Inhibitors.
Authors: Hao Zhang / Daqiang Li / Hao-Chi Hsu / Akshay Vishwanatha / Wenhu Zhan / Takafumi Yukawa / Joseph Visone / Toshihiro Imaeda / Rei Okamoto / Pavla Fajtova / Ryoma Hara / Masanori Kawasaki / ...Authors: Hao Zhang / Daqiang Li / Hao-Chi Hsu / Akshay Vishwanatha / Wenhu Zhan / Takafumi Yukawa / Joseph Visone / Toshihiro Imaeda / Rei Okamoto / Pavla Fajtova / Ryoma Hara / Masanori Kawasaki / Kenjiro Sato / Mayako Michino / Shreeya Garg / Oriana Kreutzfeld / Patrick K Tumwebaze / Stephen Orena / Martin Okitwi / Kazuyoshi Aso / Roland A Cooper / Philip J Rosenthal / Peter T Meinke / Michael Foley / Anthony J O'Donoghue / Huilin Li / Laura A Kirkman / Gang Lin /
Abstract: Malaria remains a significant global health threat, affecting millions of lives each year. The causative agents, parasites, are highly resilient and have developed resistance to nearly all existing ...Malaria remains a significant global health threat, affecting millions of lives each year. The causative agents, parasites, are highly resilient and have developed resistance to nearly all existing antimalarial drugs. The 20S proteasome core (20S), a central component of the parasite's proteostasis pathway, has emerged as a promising therapeutic target. Inhibiting 20S effectively suppresses parasite growth at multiple stages of the parasite life cycle, synergizes with artemisinin-based therapies, and shows no cross-resistance with other antimalarial drug classes. Previously, we identified a novel class of proteasome inhibitors with potent activity against 20S, which we subsequently optimized for improved potency and selectivity over human proteasomes. However, these inhibitors exhibited suboptimal pharmacokinetic properties, potentially attributable to a high number of rotatable bonds and hydrogen bond donors. Here, we describe further optimization of this inhibitor class and provide structural insights into 20S-inhibitor interactions. Cryo-EM structural studies reveal a novel binding pose of the inhibitor at the 20S β5 active site, explaining the enhanced activity of an -cap sulfonamide modification compared to an -cap amide. These findings offer insights into the development of next-generation antimalarial 20S-targeting compounds with improved drug-like properties.
History
DepositionAug 22, 2025-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72277.png

Downloads & links

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Map

FileDownload / File: emd_72277.map.gz / Format: CCP4 / Size: 216 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 384 pix.
= 317.952 Å		0.83 Å/pix.
x 384 pix.
= 317.952 Å		0.83 Å/pix.
x 384 pix.
= 317.952 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.2457457 - 2.1566653
Average (Standard dev.)0.003208936 (±0.08950908)
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_72277_msk_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_72277_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_72277_half_map_2.map
Projections & Slices
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Sample components

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Entire : Complex of Plasmodium falciparum 20S with inhibitor TDI-6245

EntireName: Complex of Plasmodium falciparum 20S with inhibitor TDI-6245
Components
  • Complex: Complex of Plasmodium falciparum 20S with inhibitor TDI-6245
    • 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: N~4~-tert-butyl-N~2~-(4-methylbenzene-1-sulfonyl)-N~1~-[2-(1-oxo-1,3-dihydro-2H-isoindol-2-yl)ethyl]-L-aspartamide

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Supramolecule #1: Complex of Plasmodium falciparum 20S with inhibitor TDI-6245

SupramoleculeName: Complex of Plasmodium falciparum 20S with inhibitor TDI-6245
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#14
Details: recombinant Plasmodium falciparum 20S complexed with inhibitor TDI-6245
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
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 (malaria parasite P. falciparum)
Molecular weightTheoretical: 29.531656 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 alpha-type subunits domain-containing protein

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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 (malaria parasite P. falciparum)
Molecular weightTheoretical: 26.556391 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 (malaria parasite P. falciparum)
Molecular weightTheoretical: 27.977664 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 (malaria parasite P. falciparum)
Molecular weightTheoretical: 27.263285 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 (malaria parasite P. falciparum)
Molecular weightTheoretical: 28.417367 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 (malaria parasite P. falciparum)
Molecular weightTheoretical: 28.742584 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 alpha-type subunits domain-containing protein

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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 (malaria parasite P. falciparum)
Molecular weightTheoretical: 29.324295 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 alpha-type subunits domain-containing protein

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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 (malaria parasite P. falciparum)
Molecular weightTheoretical: 29.143936 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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: Uncharacterized protein

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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 (malaria parasite P. falciparum)
Molecular weightTheoretical: 25.104885 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 (malaria parasite P. falciparum)
Molecular weightTheoretical: 24.533131 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 (malaria parasite P. falciparum)
Molecular weightTheoretical: 22.889105 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 (malaria parasite P. falciparum)
Molecular weightTheoretical: 23.620646 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 (malaria parasite P. falciparum)
Molecular weightTheoretical: 27.301203 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 (malaria parasite P. falciparum)
Molecular weightTheoretical: 34.822988 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 LPPAGCMWEN LYFQSSAWSH PQFEKGGGSG GGSGGSAWSH PQFEK

UniProtKB: Proteasome subunit beta

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Macromolecule #15: N~4~-tert-butyl-N~2~-(4-methylbenzene-1-sulfonyl)-N~1~-[2-(1-oxo-...

MacromoleculeName: N~4~-tert-butyl-N~2~-(4-methylbenzene-1-sulfonyl)-N~1~-[2-(1-oxo-1,3-dihydro-2H-isoindol-2-yl)ethyl]-L-aspartamide
type: ligand / ID: 15 / Number of copies: 2 / Formula: A1CRS
Molecular weightTheoretical: 500.61 Da

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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

Concentration3 mg/mL
BufferpH: 7.5 / Details: 20 mM Tris, pH 7.5, 5 mM MgCl2, and 100 mM KCl
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / 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

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 24167 / Average exposure time: 1.2 sec. / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 17354694
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8g6e

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Number images used: 124807
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8g6e


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL
Output model

PDB-9q6f:
Structure of Plasmodium falciparum 20S proteasome bound to an asparagine-ethylenediamine based inhibitor TDI6245

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