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- EMDB-10462: Leishmania tarentolae proteasome 20S subunit complexed with LXE408 -

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Basic information

Entry
Database: EMDB / ID: EMD-10462
TitleLeishmania tarentolae proteasome 20S subunit complexed with LXE408
Map data
Sample
  • Complex: Leishmania tarentolae proteasome 20S subunit complex
    • Protein or peptide: x 14 types
  • Ligand: x 1 types
Function / homology
Function and homology information


phosphoenolpyruvate carboxykinase activity / proteasome core complex / proteasome endopeptidase 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 / gluconeogenesis / ubiquitin-dependent protein catabolic process ...phosphoenolpyruvate carboxykinase activity / proteasome core complex / proteasome endopeptidase 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 / gluconeogenesis / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / hydrolase activity / protein kinase activity / protein phosphorylation / ATP binding / nucleus / cytoplasm
Similarity search - Function
Proteasome subunit alpha 3 / Proteasome subunit beta Pre3 / Proteasome subunit alpha2 / Proteasome subunit alpha4 / Proteasome subunit beta 1 / Phosphoenolpyruvate carboxykinase, N-terminal / Proteasome subunit alpha 1 / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit ...Proteasome subunit alpha 3 / Proteasome subunit beta Pre3 / Proteasome subunit alpha2 / Proteasome subunit alpha4 / Proteasome subunit beta 1 / Phosphoenolpyruvate carboxykinase, N-terminal / 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 / Ankyrin repeat-containing domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Proteasome subunit alpha type / Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit beta / Proteasome alpha 7 subunit, putative / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit family protein ...Proteasome subunit alpha type / Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit beta / Proteasome alpha 7 subunit, putative / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit family protein / Proteasome subunit alpha type / Proteasome subunit family protein / Proteasome subunit alpha type / Proteasome subunit alpha type
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsSrinivas H
CitationJournal: J Med Chem / Year: 2020
Title: Discovery and Characterization of Clinical Candidate LXE408 as a Kinetoplastid-Selective Proteasome Inhibitor for the Treatment of Leishmaniases.
Authors: Advait Nagle / Agnes Biggart / Celine Be / Honnappa Srinivas / Andreas Hein / Diana Caridha / Richard J Sciotti / Brandon Pybus / Mara Kreishman-Deitrick / Badry Bursulaya / Yin H Lai / Mu- ...Authors: Advait Nagle / Agnes Biggart / Celine Be / Honnappa Srinivas / Andreas Hein / Diana Caridha / Richard J Sciotti / Brandon Pybus / Mara Kreishman-Deitrick / Badry Bursulaya / Yin H Lai / Mu-Yun Gao / Fang Liang / Casey J N Mathison / Xiaodong Liu / Vince Yeh / Jeffrey Smith / Isabelle Lerario / Yongping Xie / Donatella Chianelli / Michael Gibney / Ashley Berman / Yen-Liang Chen / Jan Jiricek / Lauren C Davis / Xianzhong Liu / Jaime Ballard / Shilpi Khare / Fabian Kurt Eggimann / Alexandre Luneau / Todd Groessl / Michael Shapiro / Wendy Richmond / Kevin Johnson / Patrick J Rudewicz / Srinivasa P S Rao / Christopher Thompson / Tove Tuntland / Glen Spraggon / Richard J Glynne / Frantisek Supek / Christian Wiesmann / Valentina Molteni /
Abstract: Visceral leishmaniasis is responsible for up to 30,000 deaths every year. Current treatments have shortcomings that include toxicity and variable efficacy across endemic regions. Previously, we ...Visceral leishmaniasis is responsible for up to 30,000 deaths every year. Current treatments have shortcomings that include toxicity and variable efficacy across endemic regions. Previously, we reported the discovery of GNF6702, a selective inhibitor of the kinetoplastid proteasome, which cleared parasites in murine models of leishmaniasis, Chagas disease, and human African trypanosomiasis. Here, we describe the discovery and characterization of LXE408, a structurally related kinetoplastid-selective proteasome inhibitor currently in Phase 1 human clinical trials. Furthermore, we present high-resolution cryo-EM structures of the proteasome in complex with LXE408, which provides a compelling explanation for the noncompetitive mode of binding of this novel class of inhibitors of the kinetoplastid proteasome.
History
DepositionNov 7, 2019-
Header (metadata) releaseNov 27, 2019-
Map releaseAug 26, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0154
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0154
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6tcz
  • Surface level: 0.0154
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10462.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.852 Å
Density
Contour LevelBy AUTHOR: 0.0154 / Movie #1: 0.0154
Minimum - Maximum-0.07269533 - 0.110898405
Average (Standard dev.)0.0004523655 (±0.004954999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 255.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8520.8520.852
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z255.600255.600255.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0730.1110.000

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Supplemental data

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Mask #1

Fileemd_10462_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_10462_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #1

Fileemd_10462_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : Leishmania tarentolae proteasome 20S subunit complex

EntireName: Leishmania tarentolae proteasome 20S subunit complex
Components
  • Complex: Leishmania tarentolae proteasome 20S subunit complex
    • 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
    • Protein or peptide: Proteasome subunit alpha type
    • Protein or peptide: Proteasome endopeptidase complex
    • Protein or peptide: Proteasome subunit beta
    • Protein or peptide: Proteasome subunit beta
    • Protein or peptide: Proteasome subunit beta
    • Protein or peptide: Proteasome subunit family protein
    • Protein or peptide: Proteasome subunit beta
    • Protein or peptide: Proteasome subunit beta
    • Protein or peptide: Proteasome subunit beta
  • Ligand: ~{N}-[4-fluoranyl-3-[6-(3-methylpyridin-2-yl)-[1,2,4]triazolo[1,5-a]pyrimidin-2-yl]phenyl]-2,4-dimethyl-1,3-oxazole-5-carboxamide

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Supramolecule #1: Leishmania tarentolae proteasome 20S subunit complex

SupramoleculeName: Leishmania tarentolae proteasome 20S subunit complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#14
Source (natural)Organism: Leishmania donovani (eukaryote)
Recombinant expressionOrganism: Leishmania tarentolae (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: Leishmania donovani (eukaryote)
Molecular weightTheoretical: 27.178107 KDa
Recombinant expressionOrganism: Leishmania tarentolae (eukaryote)
SequenceString: MNRAGFDKYI TVFSPEGSLY QVEYAFKAVT YPGLLTVAIR CKDAVLVVTQ HLIPDRLMRP DSVTALYEVT PNIGCCMTGR APDGRALVQ RAREEASDYQ YRYGVEIPIA VLAKRMGDKA QVRTQQAGLR PMGVVSTFIG MDQSDQDGSL KPQIYTVDPA G WTGGHIAC ...String:
MNRAGFDKYI TVFSPEGSLY QVEYAFKAVT YPGLLTVAIR CKDAVLVVTQ HLIPDRLMRP DSVTALYEVT PNIGCCMTGR APDGRALVQ RAREEASDYQ YRYGVEIPIA VLAKRMGDKA QVRTQQAGLR PMGVVSTFIG MDQSDQDGSL KPQIYTVDPA G WTGGHIAC AAGKKQVEAM AFLEKRQKST ELDALTQKEA AMIALAALQS AIGTAVKAKE VEVGRCTAAN PAFQRVPNSE VE EWLTAVA EAD

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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: Leishmania donovani (eukaryote)
Molecular weightTheoretical: 25.179559 KDa
Recombinant expressionOrganism: Leishmania tarentolae (eukaryote)
SequenceString: MSEAFYGLTT FSPSGKLIQI EYATTAAGKG TTALGVKATD GVVIAAKKKA PSTLVDASSI QKVFVLDEHV GCTYSGMGPD CRVLIDSAR KNCQQYKLMY NEPIPISQLV RKISAIYQEF TQSGGVRPFG CSLLVAGVDA NGYHLYQVDP SGTFWAWKAT A IGTGSPDA ...String:
MSEAFYGLTT FSPSGKLIQI EYATTAAGKG TTALGVKATD GVVIAAKKKA PSTLVDASSI QKVFVLDEHV GCTYSGMGPD CRVLIDSAR KNCQQYKLMY NEPIPISQLV RKISAIYQEF TQSGGVRPFG CSLLVAGVDA NGYHLYQVDP SGTFWAWKAT A IGTGSPDA KAFLEKRYTV DMELEDAVHT ALLTLKEGFD GQMTSENTQV GRVVENRFEI LSVDQLRDYL DQI

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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: Leishmania donovani (eukaryote)
Molecular weightTheoretical: 32.321438 KDa
Recombinant expressionOrganism: Leishmania tarentolae (eukaryote)
SequenceString: MSHRYDSRTT TFSPEGRLYQ VEYAVEAIQQ AGTVIGVCTK DGVVLAGEKM VPHPLFDSES MQDKNTSGEK MYKIAEHIGC SVAGVTSDA YALLNYARLS ALRHQYTFQE PMAIEDLCRI LCDEKQLYTQ YGGVRPYGVS FLLVGWDRYY GYQLYSTEPS G DYSAWSAY ...String:
MSHRYDSRTT TFSPEGRLYQ VEYAVEAIQQ AGTVIGVCTK DGVVLAGEKM VPHPLFDSES MQDKNTSGEK MYKIAEHIGC SVAGVTSDA YALLNYARLS ALRHQYTFQE PMAIEDLCRI LCDEKQLYTQ YGGVRPYGVS FLLVGWDRYY GYQLYSTEPS G DYSAWSAY AIGQNDQVAH ALLKKDWHES MTLEDGMLLA LRVLGKTMDT AKIDLDRVEV AVMRKVPASN IDQLLDPFKH HP KTTPRFQ ILTRSELKPH AERADQAREA EEKAEAERQR QQEQALES

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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: Leishmania donovani (eukaryote)
Molecular weightTheoretical: 27.821605 KDa
Recombinant expressionOrganism: Leishmania tarentolae (eukaryote)
SequenceString: MSYDRAITVF SPDGHLFQVE YAQEAVKKGL AAVGVLGSDS VVIAVEKKSA VKLQDSRTIR KIYKVDANIY LAFAGLSADA RVLINKAQL ECQRFSLNYE DTMDVDMLVR YVAGVQQKST QSGGSRPFGV ATVIGGFNED GKPHLWKTDP SGMCSAWRAV A IGRHDQTV ...String:
MSYDRAITVF SPDGHLFQVE YAQEAVKKGL AAVGVLGSDS VVIAVEKKSA VKLQDSRTIR KIYKVDANIY LAFAGLSADA RVLINKAQL ECQRFSLNYE DTMDVDMLVR YVAGVQQKST QSGGSRPFGV ATVIGGFNED GKPHLWKTDP SGMCSAWRAV A IGRHDQTV IEYMEKSYKD GMSRDECVHF AIKSLLEVVE SGSRNIELLV LQYKEARYLT EEELQKFVVE VEKEREEEAA AK KKRQAEQ E

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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 / EC number: proteasome endopeptidase complex
Source (natural)Organism: Leishmania donovani (eukaryote)
Molecular weightTheoretical: 38.312316 KDa
Recombinant expressionOrganism: Leishmania tarentolae (eukaryote)
SequenceString: MLLPRLFSFP VCWSRALSLV CVYHVSLSFP SNSRRLCATP LLPLPCLCKL PAGHSPRKRC LFSFLSCFLD LTYFCIISFL HSVSCHLCF PLRRTRARHP IMFTSKSEYD RGVNTFSPEG RIFQIEYAVE AIKLGSTSLG IRTPEGVVLA AEKRVPSTLV V PSSMSKIM ...String:
MLLPRLFSFP VCWSRALSLV CVYHVSLSFP SNSRRLCATP LLPLPCLCKL PAGHSPRKRC LFSFLSCFLD LTYFCIISFL HSVSCHLCF PLRRTRARHP IMFTSKSEYD RGVNTFSPEG RIFQIEYAVE AIKLGSTSLG IRTPEGVVLA AEKRVPSTLV V PSSMSKIM EVDSHIAAVM SGMVADARIL VEHARVESQN HRFTYNEPMS VESCTLATCD LSIQFGESGG RRKLMSRPFG VS LLIAGVD EKGPQLWQTD PSGTHTRYDA QAIGGGAEAA QSVFTERYHR NMTLEEGETL AVDILKQVME DQLSPENIEV AVV RADDGK LHMYTPTEIK AIMSRMPE

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Macromolecule #6: Proteasome subunit alpha type

MacromoleculeName: Proteasome subunit alpha type / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Leishmania donovani (eukaryote)
Molecular weightTheoretical: 47.978633 KDa
Recombinant expressionOrganism: Leishmania tarentolae (eukaryote)
SequenceString: MQSRKGEGWR DTGTDSLPPF SFCCSPAFSS PLAFGGEGAD GCAYILTHVC RYACIAALTL HSEGAERHMR VCVCVRRCAY NEMVLHQVV AFASLAPALH PLSPLPLPCM ATTHACCGLR VRSFSLKKSE KKNQQRRLQA PDLSQKTRTR TQKEKQTLQI Y LRCVMFKN ...String:
MQSRKGEGWR DTGTDSLPPF SFCCSPAFSS PLAFGGEGAD GCAYILTHVC RYACIAALTL HSEGAERHMR VCVCVRRCAY NEMVLHQVV AFASLAPALH PLSPLPLPCM ATTHACCGLR VRSFSLKKSE KKNQQRRLQA PDLSQKTRTR TQKEKQTLQI Y LRCVMFKN EYDSDITTWS PTGRLFQIEY ANEAVNNGSA TVGVKGKNFV VLAALKRSPV AELSSYQEKV FEIDEHVGMS IS GLVADGR VLARYLRTEC MNYRYMYSNG MPMNQMADMI GEKHQRHIQC SGKRPFGVGL LLAGYDRQGP HLYQTVPSGD VYD YKATAM GVRSQASRTY LERHFEHFSD CTLDELVTHA LKALASATSE GIELNVKNTT IAIVGKDTPF TIFEEESARK YLDG FKMRP EDRVAVAEED EEMLHEQPLD VEE

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Macromolecule #7: Proteasome endopeptidase complex

MacromoleculeName: Proteasome endopeptidase complex / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Leishmania donovani (eukaryote)
Molecular weightTheoretical: 25.591826 KDa
Recombinant expressionOrganism: Leishmania tarentolae (eukaryote)
SequenceString: MAGTGSGHDQ STDVFSAEGR VFQVEYAGKA VDNSSTAVAA CCKDGVVVAV EKVHTSRMLE KGSNNRIHAV DRQAGICICG LLPDGRAIV SRARQEAENS RDIFATPIRG SVLANRVGEF MHAYTTHFAY RPFGCSAIIA SYADDGPQLF VSDPSGTVAG Y YGVALGKA ...String:
MAGTGSGHDQ STDVFSAEGR VFQVEYAGKA VDNSSTAVAA CCKDGVVVAV EKVHTSRMLE KGSNNRIHAV DRQAGICICG LLPDGRAIV SRARQEAENS RDIFATPIRG SVLANRVGEF MHAYTTHFAY RPFGCSAIIA SYADDGPQLF VSDPSGTVAG Y YGVALGKA KTVAKSELEK LDFSSLTCDE AVGKLASILH EVHDKQKDKL YEVEVAWVCD KSDRKFVHVP ADMVPAETSH

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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: Leishmania donovani (eukaryote)
Molecular weightTheoretical: 30.28001 KDa
Recombinant expressionOrganism: Leishmania tarentolae (eukaryote)
SequenceString: MLQRPDHTLL QEPAYPKDIA QKLTENGPAQ AGKQLFQPDP AVIDPQLSKA VSLGTTILAV SYNGGVVLAA DSRTSSGTYV VNRASNKLT KLTKKIYCCR SGSAADTQAL AERVSNYLGS YQTDIGAGVN VATAANLFQK MCYMNRWNIS AGIIVAGYDP I NGGSVYSI ...String:
MLQRPDHTLL QEPAYPKDIA QKLTENGPAQ AGKQLFQPDP AVIDPQLSKA VSLGTTILAV SYNGGVVLAA DSRTSSGTYV VNRASNKLT KLTKKIYCCR SGSAADTQAL AERVSNYLGS YQTDIGAGVN VATAANLFQK MCYMNRWNIS AGIIVAGYDP I NGGSVYSI PSGGSCVKLD YALGGSGSIF LYSFFDANYK PGMSKSECVA FCQRAVAHAY SRDGSSGGLI RTITLDADEP ED QTIPWNR SPYCMEKDPK YVTQATQNQP FSSSAKITGN RMSSTG

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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 / EC number: proteasome endopeptidase complex
Source (natural)Organism: Leishmania donovani (eukaryote)
Molecular weightTheoretical: 27.60357 KDa
Recombinant expressionOrganism: Leishmania tarentolae (eukaryote)
SequenceString: MPGFNFENVQ RNLNLEGEGY SAPRTLKTGT TIVGVVYRDG VVLGADTRAT EGSIVADKRC RKIHYMAPNI MCCGAGTSAD TEAVTNMVS SHLALHRLET GKQSRVLEAL TLLKRHLYRY QGHVSAALVL GGVDVEGPFL ATIAPHGSTD RLPFVTMGSG S IAAMAQLE ...String:
MPGFNFENVQ RNLNLEGEGY SAPRTLKTGT TIVGVVYRDG VVLGADTRAT EGSIVADKRC RKIHYMAPNI MCCGAGTSAD TEAVTNMVS SHLALHRLET GKQSRVLEAL TLLKRHLYRY QGHVSAALVL GGVDVEGPFL ATIAPHGSTD RLPFVTMGSG S IAAMAQLE AAYKDNMTCE EAKELVASAI RKGIFNDPYS GTQVDVCVIT KDKTELTIGY DKPNERMYPR QEVLLPPGTT PV LKEEIRQ LVDIVDA

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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 / EC number: proteasome endopeptidase complex
Source (natural)Organism: Leishmania donovani (eukaryote)
Molecular weightTheoretical: 22.470887 KDa
Recombinant expressionOrganism: Leishmania tarentolae (eukaryote)
SequenceString: MSIMAYSGGS VMAMAGKECF VIISDNRLGE QLKTISTEVP KLHVVNDSIV YGLTGLRTDQ QTFANKVQFR TEMYKLREER DITGKAFAA MITSMLYEAR FGPWFVEPVI GSIDKSTGEV YLCATDLIGA PCEPEDYVCA GTAAESLHGM CEALWRPGMS P EELFEIAA ...String:
MSIMAYSGGS VMAMAGKECF VIISDNRLGE QLKTISTEVP KLHVVNDSIV YGLTGLRTDQ QTFANKVQFR TEMYKLREER DITGKAFAA MITSMLYEAR FGPWFVEPVI GSIDKSTGEV YLCATDLIGA PCEPEDYVCA GTAAESLHGM CEALWRPGMS P EELFEIAA QAMLSACDRD SLSGYGAVAM IVTKDKVTTR LIKGRKD

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Macromolecule #11: Proteasome subunit family protein

MacromoleculeName: Proteasome subunit family protein / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania donovani (eukaryote)
Molecular weightTheoretical: 23.065291 KDa
Recombinant expressionOrganism: Leishmania tarentolae (eukaryote)
SequenceString: MAETAIAFRC KDYVMVAAAG LNAFYYIKIT DAEDKITQLD THQLVACTGE NGPRVNFTEY IKCNLALNRM RQHGRHSSCE STANFMRNC LASAIRSREG AYQVNCLFAG YDTPVSEDDD GVVGPQLFYM DYLGTLQAVP YGCHGYGACF VTALLDRLWR P DLSQQEGL ...String:
MAETAIAFRC KDYVMVAAAG LNAFYYIKIT DAEDKITQLD THQLVACTGE NGPRVNFTEY IKCNLALNRM RQHGRHSSCE STANFMRNC LASAIRSREG AYQVNCLFAG YDTPVSEDDD GVVGPQLFYM DYLGTLQAVP YGCHGYGACF VTALLDRLWR P DLSQQEGL ELMQKCCDEV KRRVIISNSY FFVKAVTKNG VEVITAVH

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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 / EC number: proteasome endopeptidase complex
Source (natural)Organism: Leishmania donovani (eukaryote)
Molecular weightTheoretical: 33.704867 KDa
Recombinant expressionOrganism: Leishmania tarentolae (eukaryote)
SequenceString: MFADFEAVTS SNFTLDDCPR VGPFTYHNMD EDTLEEPLSL CSYRRAPQQT DERSPASCDA VTADPLDSSR YLHGENRCWT LKVSCPVPR AIPKLDMKKG TTTLAFRFNG GIIVAVDSRA STGQYIASQT VMKVLEINDY LLGTLAGGAA DCQYWERVLG M ECRLWELR ...String:
MFADFEAVTS SNFTLDDCPR VGPFTYHNMD EDTLEEPLSL CSYRRAPQQT DERSPASCDA VTADPLDSSR YLHGENRCWT LKVSCPVPR AIPKLDMKKG TTTLAFRFNG GIIVAVDSRA STGQYIASQT VMKVLEINDY LLGTLAGGAA DCQYWERVLG M ECRLWELR NGSRITVAAA SKILANITYA YRNHGLSMGT MVAGWDQFGP SLYYVDDKGS RVKQDLFSVG SGSIYAYGVL DT GYRKDLS VEDACDLARR SIFHATYRDG ASGGIVTVYH VHEKGWTKIS RDDQTKLYHR YFPSQ

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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: Leishmania donovani (eukaryote)
Molecular weightTheoretical: 37.67691 KDa
Recombinant expressionOrganism: Leishmania tarentolae (eukaryote)
SequenceString: MASSSPPLLP FSSFVVAVVA IHLSFRVFCV GAQSLCKCCS CVPACALPLC FSSSPSVSAE DVALALFAHP KVLTHRPTAR YSPILSLLH YAVMIEDHAE YGHNYYPQKL ASSTLTLPQQ GAKQQQWSPY QDNGGTTAAI AGKDFVILAG DTRLNGDFCL H SRHDQSKI ...String:
MASSSPPLLP FSSFVVAVVA IHLSFRVFCV GAQSLCKCCS CVPACALPLC FSSSPSVSAE DVALALFAHP KVLTHRPTAR YSPILSLLH YAVMIEDHAE YGHNYYPQKL ASSTLTLPQQ GAKQQQWSPY QDNGGTTAAI AGKDFVILAG DTRLNGDFCL H SRHDQSKI FQLTPYTYMA SNGMQADRLQ LQQMLKYRVK WYKYNNGGKV PSTKAIAQLM STMLYHRRFF PYYTFNMVVG LD EEGHGVC YSYDAVGSTE PFLYGTRGSA ASFVEPLLDC LINRQHMTSQ APPEMTKEET LAMLKNAFTG AAERDIYTGD SVS FFIITK DGVQQESFEL RKD

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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: Leishmania donovani (eukaryote)
Molecular weightTheoretical: 24.737232 KDa
Recombinant expressionOrganism: Leishmania tarentolae (eukaryote)
SequenceString: MASGGSVIAI KYKGGVLMAA DTLLSYGSLA KWPNIPRIRL LGSHSAVCAT GSYADFQMMA KQVEDNIERQ KMYHNVDELS PSEVFSYLH RSIYQKRCDF DPCLCQMVFI GVRDGETFLA GVDDVGTRWE DDCIATGYGA YIALPLLRQA LEKNPDGLSR G EAMRILTD ...String:
MASGGSVIAI KYKGGVLMAA DTLLSYGSLA KWPNIPRIRL LGSHSAVCAT GSYADFQMMA KQVEDNIERQ KMYHNVDELS PSEVFSYLH RSIYQKRCDF DPCLCQMVFI GVRDGETFLA GVDDVGTRWE DDCIATGYGA YIALPLLRQA LEKNPDGLSR G EAMRILTD CLRVLFYREC RAINKFQVAD AASDGVRISE PFDVETHWEY EGYCFEKTAI IR

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Macromolecule #15: ~{N}-[4-fluoranyl-3-[6-(3-methylpyridin-2-yl)-[1,2,4]triazolo[1,5...

MacromoleculeName: ~{N}-[4-fluoranyl-3-[6-(3-methylpyridin-2-yl)-[1,2,4]triazolo[1,5-a]pyrimidin-2-yl]phenyl]-2,4-dimethyl-1,3-oxazole-5-carboxamide
type: ligand / ID: 15 / Number of copies: 2 / Formula: N2E
Molecular weightTheoretical: 443.433 Da
Chemical component information

ChemComp-N2E:
~{N}-[4-fluoranyl-3-[6-(3-methylpyridin-2-yl)-[1,2,4]triazolo[1,5-a]pyrimidin-2-yl]phenyl]-2,4-dimethyl-1,3-oxazole-5-carboxamide

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 1.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 38000
FSC plot (resolution estimation)

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