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- EMDB-23575: Structure of Plasmodium falciparum 20S proteasome with bound MPI-5 -

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Basic information

Entry
Database: EMDB / ID: EMD-23575
TitleStructure of Plasmodium falciparum 20S proteasome with bound MPI-5
Map dataStructure of Plasmodium falciparum 20S proteasome with bound ML052
Sample
  • Complex: Plasmodium falciparum 20S proteasome complexed with ML052
    • Protein or peptide: x 13 types
  • Protein or peptide: x 1 types
  • Ligand: x 1 types
Function / homology
Function and homology information


Cross-presentation of soluble exogenous antigens (endosomes) / : / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / KEAP1-NFE2L2 pathway / UCH proteinases / Ub-specific processing proteases / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / Neutrophil degranulation ...Cross-presentation of soluble exogenous antigens (endosomes) / : / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / KEAP1-NFE2L2 pathway / UCH proteinases / Ub-specific processing proteases / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / Neutrophil degranulation / proteasome core complex / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / proteasomal protein catabolic process / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / hydrolase activity / nucleus / cytosol / cytoplasm
Similarity search - Function
Proteasome subunit beta 1 / 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 beta 1 / 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 beta / Proteasome subunit alpha type-2, putative / 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, putative / 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 (malaria parasite P. falciparum) / Plasmodium falciparum (isolate 3D7) (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsHanssen E / Liu B / Leis AP / Xie SC / Morton CJ / Metcalfe RD / Tilley L / Griffin MDW
Funding support Australia, United States, 2 items
OrganizationGrant numberCountry
Australian Research Council (ARC)FL150100106 Australia
Global Health Innovative Technology FundRFP-HTLP-H2019-101 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Design of proteasome inhibitors with oral efficacy in vivo against and selectivity over the human proteasome.
Authors: Stanley C Xie / Riley D Metcalfe / Hirotake Mizutani / Tanya Puhalovich / Eric Hanssen / Craig J Morton / Yawei Du / Con Dogovski / Shih-Chung Huang / Jeffrey Ciavarri / Paul Hales / Robert ...Authors: Stanley C Xie / Riley D Metcalfe / Hirotake Mizutani / Tanya Puhalovich / Eric Hanssen / Craig J Morton / Yawei Du / Con Dogovski / Shih-Chung Huang / Jeffrey Ciavarri / Paul Hales / Robert J Griffin / Lawrence H Cohen / Bei-Ching Chuang / Sergio Wittlin / Ioanna Deni / Tomas Yeo / Kurt E Ward / Daniel C Barry / Boyin Liu / David L Gillett / Benigno F Crespo-Fernandez / Sabine Ottilie / Nimisha Mittal / Alisje Churchyard / Daniel Ferguson / Anna Caroline C Aguiar / Rafael V C Guido / Jake Baum / Kirsten K Hanson / Elizabeth A Winzeler / Francisco-Javier Gamo / David A Fidock / Delphine Baud / Michael W Parker / Stephen Brand / Lawrence R Dick / Michael D W Griffin / Alexandra E Gould / Leann Tilley /
Abstract: The proteasome is a potential antimalarial drug target. We have identified a series of amino-amide boronates that are potent and specific inhibitors of the 20S proteasome (20S) β5 active site and ...The proteasome is a potential antimalarial drug target. We have identified a series of amino-amide boronates that are potent and specific inhibitors of the 20S proteasome (20S) β5 active site and that exhibit fast-acting antimalarial activity. They selectively inhibit the growth of compared with a human cell line and exhibit high potency against field isolates of and They have a low propensity for development of resistance and possess liver stage and transmission-blocking activity. Exemplar compounds, MPI-5 and MPI-13, show potent activity against infections in a SCID mouse model with an oral dosing regimen that is well tolerated. We show that MPI-5 binds more strongly to 20S than to human constitutive 20S (20Sc). Comparison of the cryo-electron microscopy (EM) structures of 20S and 20Sc in complex with MPI-5 and 20S in complex with the clinically used anti-cancer agent, bortezomib, reveal differences in binding modes that help to explain the selectivity. Together, this work provides insights into the 20S proteasome in , underpinning the design of potent and selective antimalarial proteasome inhibitors.
History
DepositionMar 5, 2021-
Header (metadata) releaseSep 22, 2021-
Map releaseSep 22, 2021-
UpdateApr 13, 2022-
Current statusApr 13, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 10
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 10
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7lxu
  • Surface level: 10
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23575.png

Downloads & links

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Map

FileDownload / File: emd_23575.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of Plasmodium falciparum 20S proteasome with bound ML052
Voxel sizeX=Y=Z: 1.31 Å
Density
Contour LevelBy AUTHOR: 5.0 / Movie #1: 10
Minimum - Maximum-22.977833 - 45.61232
Average (Standard dev.)4.7349843e-14 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 524.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.311.311.31
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z524.000524.000524.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-22.97845.6120.000

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Supplemental data

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Additional map: Additional map

Fileemd_23575_additional_1.map
AnnotationAdditional map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-volume 1

Fileemd_23575_half_map_1.map
Annotationhalf-volume 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-volume 2

Fileemd_23575_half_map_2.map
Annotationhalf-volume 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Plasmodium falciparum 20S proteasome complexed with ML052

EntireName: Plasmodium falciparum 20S proteasome complexed with ML052
Components
  • Complex: Plasmodium falciparum 20S proteasome complexed with ML052
    • Protein or peptide: 20S proteasome alpha-1 subunit
    • Protein or peptide: 20S proteasome alpha-2 subunit
    • Protein or peptide: 20S proteasome alpha-3 subunit
    • Protein or peptide: 20S proteasome alpha-4 subunit
    • Protein or peptide: 20S proteasome alpha-5 subunit
    • Protein or peptide: 20S proteasome alpha-6 subunit
    • Protein or peptide: 20S proteasome alpha-7 subunit
    • Protein or peptide: 20S proteasome beta-1 subunit
    • Protein or peptide: 20S proteasome beta-2 subunit
    • Protein or peptide: 20S proteasome beta-3 subunit
    • Protein or peptide: 20S proteasome beta-4 subunit
    • Protein or peptide: 20S proteasome beta-6 subunit
    • Protein or peptide: 20S proteasome beta-7 subunit
  • Protein or peptide: 20S proteasome beta-5 subunit
  • Ligand: N-[(1R)-2-([1,1'-biphenyl]-4-yl)-1-boronoethyl]-1-methyl-L-prolinamide

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Supramolecule #1: Plasmodium falciparum 20S proteasome complexed with ML052

SupramoleculeName: Plasmodium falciparum 20S proteasome complexed with ML052
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11, #13-#14
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Molecular weightTheoretical: 700 KDa

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Macromolecule #1: 20S proteasome alpha-1 subunit

MacromoleculeName: 20S proteasome alpha-1 subunit / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Plasmodium falciparum (isolate 3D7) (eukaryote) / Strain: isolate 3D7
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

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Macromolecule #2: 20S proteasome alpha-2 subunit

MacromoleculeName: 20S proteasome alpha-2 subunit / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Plasmodium falciparum (isolate 3D7) (eukaryote) / Strain: isolate 3D7
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

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Macromolecule #3: 20S proteasome alpha-3 subunit

MacromoleculeName: 20S proteasome alpha-3 subunit / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Plasmodium falciparum (isolate 3D7) (eukaryote) / Strain: isolate 3D7
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

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Macromolecule #4: 20S proteasome alpha-4 subunit

MacromoleculeName: 20S proteasome alpha-4 subunit / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Plasmodium falciparum (isolate 3D7) (eukaryote) / Strain: isolate 3D7
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

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Macromolecule #5: 20S proteasome alpha-5 subunit

MacromoleculeName: 20S proteasome alpha-5 subunit / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Plasmodium falciparum (isolate 3D7) (eukaryote) / Strain: isolate 3D7
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

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Macromolecule #6: 20S proteasome alpha-6 subunit

MacromoleculeName: 20S proteasome alpha-6 subunit / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Plasmodium falciparum (isolate 3D7) (eukaryote) / Strain: isolate 3D7
Molecular weightTheoretical: 28.871697 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 VQNEANE

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Macromolecule #7: 20S proteasome alpha-7 subunit

MacromoleculeName: 20S proteasome alpha-7 subunit / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Plasmodium falciparum (isolate 3D7) (eukaryote) / Strain: isolate 3D7
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

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Macromolecule #8: 20S proteasome beta-1 subunit

MacromoleculeName: 20S proteasome beta-1 subunit / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Plasmodium falciparum (isolate 3D7) (eukaryote) / Strain: isolate 3D7
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

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Macromolecule #9: 20S proteasome beta-2 subunit

MacromoleculeName: 20S proteasome beta-2 subunit / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Plasmodium falciparum (isolate 3D7) (eukaryote) / Strain: isolate 3D7
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

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Macromolecule #10: 20S proteasome beta-3 subunit

MacromoleculeName: 20S proteasome beta-3 subunit / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Plasmodium falciparum (isolate 3D7) (eukaryote) / Strain: isolate 3D7
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

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Macromolecule #11: 20S proteasome beta-4 subunit

MacromoleculeName: 20S proteasome beta-4 subunit / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Plasmodium falciparum (isolate 3D7) (eukaryote) / Strain: isolate 3D7
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

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Macromolecule #12: 20S proteasome beta-5 subunit

MacromoleculeName: 20S proteasome beta-5 subunit / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Plasmodium falciparum (isolate 3D7) (eukaryote) / Strain: isolate 3D7
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

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Macromolecule #13: 20S proteasome beta-6 subunit

MacromoleculeName: 20S proteasome beta-6 subunit / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Plasmodium falciparum (isolate 3D7) (eukaryote) / Strain: isolate 3D7
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

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Macromolecule #14: 20S proteasome beta-7 subunit

MacromoleculeName: 20S proteasome beta-7 subunit / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Plasmodium falciparum (isolate 3D7) (eukaryote) / Strain: isolate 3D7
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

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Macromolecule #15: N-[(1R)-2-([1,1'-biphenyl]-4-yl)-1-boronoethyl]-1-methyl-L-prolinamide

MacromoleculeName: N-[(1R)-2-([1,1'-biphenyl]-4-yl)-1-boronoethyl]-1-methyl-L-prolinamide
type: ligand / ID: 15 / Number of copies: 2 / Formula: YHD
Molecular weightTheoretical: 352.235 Da
Chemical component information

ChemComp-YHD:
N-[(1R)-2-([1,1'-biphenyl]-4-yl)-1-boronoethyl]-1-methyl-L-prolinamide

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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: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware:
Namedetails
RELION (ver. 3)wraper for motioncorr2, particle polishing
MotionCorr2 (ver. 2)motion correction
cryoSPARC (ver. 2.15)particle picking, 2D classes, 3D classes, refinements
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 38738
FSC plot (resolution estimation)

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