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- EMDB-73509: Structure of the Plasmodium falciparum 20S proteasome in complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-73509
TitleStructure of the Plasmodium falciparum 20S proteasome in complex with a beta5-selective covalent syringolin analogue inhibitor.
Map dataStructure of the Plasmodium falciparum 20S proteasome in complex with a beta5-selective covalent syringolin analogue inhibitor.
Sample
  • Complex: Plasmodium falciparum 20S proteasome
    • Protein or peptide: x 14 types
  • Ligand: x 1 types
KeywordsProteasome / 20S / Inhibitor / Plasmodium / Covalent / HYDROLASE
Function / homology
Function and homology information


ER-Phagosome pathway / Cross-presentation of soluble exogenous antigens (endosomes) / Proteasome assembly / Antigen processing: Ub, ATP-independent proteasomal degradation / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / UCH proteinases / Ub-specific processing proteases ...ER-Phagosome pathway / Cross-presentation of soluble exogenous antigens (endosomes) / Proteasome assembly / Antigen processing: Ub, ATP-independent proteasomal degradation / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / UCH proteinases / Ub-specific processing proteases / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / MAPK6/MAPK4 signaling / ABC-family protein mediated transport / AUF1 (hnRNP D0) binds and destabilizes mRNA / Neutrophil degranulation / proteasome core complex / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / endopeptidase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / hydrolase activity / nucleus / cytoplasm / cytosol
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 A N-terminal signature ...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 beta / Proteasome subunit alpha type-2 / Proteasome subunit alpha type-3, putative / Proteasome subunit beta / Proteasome subunit beta type-6, putative / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit alpha type-6, putative / Proteasome subunit alpha type / Proteasome subunit alpha type ...Proteasome subunit beta / Proteasome subunit alpha type-2 / Proteasome subunit alpha type-3, putative / Proteasome subunit beta / Proteasome subunit beta type-6, putative / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit alpha type-6, putative / Proteasome subunit alpha type / Proteasome subunit alpha type / Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit alpha type-1, putative / Proteasome subunit beta
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsYan NL / Gu X / Fajtova P / Tse E / Melo A / Southworth DR / O'Donoghue A / Sello JK / Gestwicki JE
Funding support1 items
OrganizationGrant numberCountry
Other private
CitationJournal: J Med Chem / Year: 2026
Title: An Optimized Route to the Syringolin Natural Products Enables Combinatorial Synthesis of Selective, Bioactive Inhibitors of the 20S Proteasome.
Authors: Xilin Gu / Pavla Fajtova / Nicholas L Yan / Aditi Saxena / Fan Fei / Jiyun Zhu / Eric Tse / Arthur Melo / Euna Yoo / Nathan H Buchwald / Daniel R Southworth / Matthew Bogyo / Joseph L Derisi ...Authors: Xilin Gu / Pavla Fajtova / Nicholas L Yan / Aditi Saxena / Fan Fei / Jiyun Zhu / Eric Tse / Arthur Melo / Euna Yoo / Nathan H Buchwald / Daniel R Southworth / Matthew Bogyo / Joseph L Derisi / Jason E Gestwicki / Anthony J O'Donoghue / Jason K Sello /
Abstract: The syringolin natural products are covalent inhibitors of the 20S proteasome that inspire therapeutic development. Here, we report a new route to the syringolins amenable to solution and solid-phase ...The syringolin natural products are covalent inhibitors of the 20S proteasome that inspire therapeutic development. Here, we report a new route to the syringolins amenable to solution and solid-phase synthesis that overcomes a problematic macrocyclization. Exploiting our synthetic approach and substrate mimicry models for proteasome inhibition by the syringolins, we generated a collection of hypothetically selective inhibitors of the proteasome, which is an emerging target for antimalarial drugs. We identified compounds from the library having high second-order rate constants for proteasome inhibition and nanomolar antiparasitic activity. They exhibited selectivity for the proteasome over the human proteasome. We solved cryo-EM structures of an inhibitor bound to both 20S proteasomes, revealing key contacts favoring species-selective inhibition. Together, this work provides an improved route to syringolin analogs, sheds new light on substrate mimicry by the syringolins, and provides a structural basis for the pursuit of new antimalarial drugs.
History
DepositionOct 23, 2025-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73509.png

Downloads & links

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Map

FileDownload / File: emd_73509.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the Plasmodium falciparum 20S proteasome in complex with a beta5-selective covalent syringolin analogue inhibitor.
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 300 pix.
= 333.6 Å		1.11 Å/pix.
x 300 pix.
= 333.6 Å		1.11 Å/pix.
x 300 pix.
= 333.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.112 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-1.9997914 - 3.7272131
Average (Standard dev.)0.00303545 (±0.1586024)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 333.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_73509_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_73509_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Plasmodium falciparum 20S proteasome

EntireName: Plasmodium falciparum 20S proteasome
Components
  • Complex: Plasmodium falciparum 20S proteasome
    • 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 endopeptidase complex
    • Protein or peptide: Proteasome subunit alpha type-3, putative
    • Protein or peptide: Proteasome subunit beta
    • Protein or peptide: Proteasome subunit beta
    • Protein or peptide: Proteasome endopeptidase complex
    • Protein or peptide: Proteasome endopeptidase complex
    • Protein or peptide: Proteasome subunit beta type-6, putative
    • 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: methyl N-{[(2R)-1-({(5R,8R)-5-[(3-fluorophenyl)methyl]-2,7-dioxo-1,6-diazacyclododecan-8-yl}amino)-1-oxo-3-phenylpropan-2-yl]carbamoyl}-L-valinate

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Supramolecule #1: Plasmodium falciparum 20S proteasome

SupramoleculeName: Plasmodium falciparum 20S proteasome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6, #8-#13, #7, #14
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)

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Macromolecule #1: Proteasome subunit alpha type

MacromoleculeName: Proteasome subunit alpha type / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
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 #2: Proteasome subunit alpha type

MacromoleculeName: Proteasome subunit alpha type / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
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 #3: Proteasome subunit alpha type

MacromoleculeName: Proteasome subunit alpha type / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
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 #4: Proteasome endopeptidase complex

MacromoleculeName: Proteasome endopeptidase complex / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
Molecular weightTheoretical: 28.871697 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 VQNEANE

UniProtKB: Proteasome subunit alpha type-1, putative

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Macromolecule #5: Proteasome subunit alpha type-3, putative

MacromoleculeName: Proteasome subunit alpha type-3, putative / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
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 subunit alpha type-3, putative

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Macromolecule #6: Proteasome subunit beta

MacromoleculeName: Proteasome subunit beta / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
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 #7: Proteasome subunit beta

MacromoleculeName: Proteasome subunit beta / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
Molecular weightTheoretical: 30.630432 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MVIASDESFM NEIDNLINDV EDERIDNDEL EFCVAPVNVP RNFIKYAQTQ NKKLFDFHKG TTTLAFKFKD GIIVAVDSRA SMGSFISSQ NVEKIIEINK NILGTMAGGA ADCLYWEKYL GKIIKIYELR NNEKISVRAA STILSNILYQ YKGYGLCCGI I LSGYDHTG ...String:
MVIASDESFM NEIDNLINDV EDERIDNDEL EFCVAPVNVP RNFIKYAQTQ NKKLFDFHKG TTTLAFKFKD GIIVAVDSRA SMGSFISSQ NVEKIIEINK NILGTMAGGA ADCLYWEKYL GKIIKIYELR NNEKISVRAA STILSNILYQ YKGYGLCCGI I LSGYDHTG FNMFYVDDSG KKVEGNLFSC GSGSTYAYSI LDSAYDYNLN LDQAVELARN AIYHATFRDG GSGGKVRVFH IH KNGYDKI IEGEDVFDLH YHYTNPEQKD QYVM

UniProtKB: Proteasome subunit beta

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Macromolecule #8: Proteasome subunit beta

MacromoleculeName: Proteasome subunit beta / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
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 #9: Proteasome endopeptidase complex

MacromoleculeName: Proteasome endopeptidase complex / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
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 subunit alpha type-6, putative

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Macromolecule #10: Proteasome endopeptidase complex

MacromoleculeName: Proteasome endopeptidase complex / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
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 #11: Proteasome subunit beta type-6, putative

MacromoleculeName: Proteasome subunit beta type-6, putative / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
Molecular weightTheoretical: 32.641682 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDVVNESQIK CHEEKSWDDE YDIKTPISDG TTIIGIIYDN GVMLACDSRT SSGTFISNKC SRKINRINEN LYVCRSGASA HSQKIIEII KHYCVSMKNE NRKKGRFHEG ETIYDETTYD EEIDIDSINY LDYNNNNDNN LVTKNKYFYE DKFNDYNPLV E NVAHITKK ...String:
MDVVNESQIK CHEEKSWDDE YDIKTPISDG TTIIGIIYDN GVMLACDSRT SSGTFISNKC SRKINRINEN LYVCRSGASA HSQKIIEII KHYCVSMKNE NRKKGRFHEG ETIYDETTYD EEIDIDSINY LDYNNNNDNN LVTKNKYFYE DKFNDYNPLV E NVAHITKK IIYTNNNFLS CALIFGGYDK IKKQQLYAVN LNGSIIEKHD FAVSGSGSIY IQSYLQDKYK KFMTKKECFN LI LNCVKYA MHNDNSSGGL IRIVNITKSF VEEFTVVNTQ MNFQY

UniProtKB: Proteasome subunit beta type-6, putative

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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 3D7 (eukaryote)
Molecular weightTheoretical: 29.999557 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKLEYINILK EENGGYNFDN LKRNEILKEK GVKFPQFRKT GTTICGLVCQ NAVILGADTR ATEGPIVADK NCSKLHYISK NIWCAGAGV AGDLEHTTLW LQHNVELHRL NTNTQPRVSM CVSRLTQELF KYQGYKVCAI VLGGVDVNGP QLYGIHPHGS S CLLPFTAL ...String:
MKLEYINILK EENGGYNFDN LKRNEILKEK GVKFPQFRKT GTTICGLVCQ NAVILGADTR ATEGPIVADK NCSKLHYISK NIWCAGAGV AGDLEHTTLW LQHNVELHRL NTNTQPRVSM CVSRLTQELF KYQGYKVCAI VLGGVDVNGP QLYGIHPHGS S CLLPFTAL GSGSLNAMAV LEAKYRDNMT IEEGKNLVCE AICAGIFNDL GSGGNVDICV ITKDSYQHIR PYKEPNMRLY HL PHPTIYP KGTTPILSEK IEYIKKFISV EDA

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 / EC number: proteasome endopeptidase complex
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
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 #14: Proteasome subunit beta

MacromoleculeName: Proteasome subunit beta / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
Molecular weightTheoretical: 30.909893 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 LPPAGCMW

UniProtKB: Proteasome subunit beta

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Macromolecule #15: methyl N-{[(2R)-1-({(5R,8R)-5-[(3-fluorophenyl)methyl]-2,7-dioxo-...

MacromoleculeName: methyl N-{[(2R)-1-({(5R,8R)-5-[(3-fluorophenyl)methyl]-2,7-dioxo-1,6-diazacyclododecan-8-yl}amino)-1-oxo-3-phenylpropan-2-yl]carbamoyl}-L-valinate
type: ligand / ID: 15 / Number of copies: 2 / Formula: A1CY6
Molecular weightTheoretical: 625.731 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 46.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 36364
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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
Output model

PDB-9yuy:
Structure of the Plasmodium falciparum 20S proteasome in complex with a beta5-selective covalent syringolin analogue inhibitor.

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