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- EMDB-4590: Leishmania tarentolae proteasome 20S subunit complexed with GSK3494245 -

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Basic information

Entry
Database: EMDB / ID: EMD-4590
TitleLeishmania tarentolae proteasome 20S subunit complexed with GSK3494245
Map dataThis is the sharpened EM map which was used for building the protein coordinates
Sample
  • Complex: Proteasome 20S subunit
    • Protein or peptide: x 14 types
  • Ligand: x 2 types
KeywordsProteasome 20S subunit / hydrolase
Function / homology
Function and homology information


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 / proteolysis involved in protein catabolic process / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / hydrolase activity ...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 / proteolysis involved in protein catabolic process / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / hydrolase activity / nucleus / cytoplasm
Similarity search - Function
Proteasome subunit alpha 1 / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature ...Proteasome subunit alpha 1 / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit alpha type / Putative proteasome alpha 7 subunit / Proteasome subunit beta / Proteasome subunit beta ...Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit alpha type / Putative proteasome alpha 7 subunit / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit alpha type
Similarity search - Component
Biological speciesLeishmania tarentolae (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsRowland P / Goswami P
CitationJournal: Proc Natl Acad Sci U S A / Year: 2019
Title: Preclinical candidate for the treatment of visceral leishmaniasis that acts through proteasome inhibition.
Authors: Susan Wyllie / Stephen Brand / Michael Thomas / Manu De Rycker / Chun-Wa Chung / Imanol Pena / Ryan P Bingham / Juan A Bueren-Calabuig / Juan Cantizani / David Cebrian / Peter D Craggs / ...Authors: Susan Wyllie / Stephen Brand / Michael Thomas / Manu De Rycker / Chun-Wa Chung / Imanol Pena / Ryan P Bingham / Juan A Bueren-Calabuig / Juan Cantizani / David Cebrian / Peter D Craggs / Liam Ferguson / Panchali Goswami / Judith Hobrath / Jonathan Howe / Laura Jeacock / Eun-Jung Ko / Justyna Korczynska / Lorna MacLean / Sujatha Manthri / Maria S Martinez / Lydia Mata-Cantero / Sonia Moniz / Andrea Nühs / Maria Osuna-Cabello / Erika Pinto / Jennifer Riley / Sharon Robinson / Paul Rowland / Frederick R C Simeons / Yoko Shishikura / Daniel Spinks / Laste Stojanovski / John Thomas / Stephen Thompson / Elisabet Viayna Gaza / Richard J Wall / Fabio Zuccotto / David Horn / Michael A J Ferguson / Alan H Fairlamb / Jose M Fiandor / Julio Martin / David W Gray / Timothy J Miles / Ian H Gilbert / Kevin D Read / Maria Marco / Paul G Wyatt /
Abstract: Visceral leishmaniasis (VL), caused by the protozoan parasites and , is one of the major parasitic diseases worldwide. There is an urgent need for new drugs to treat VL, because current therapies ...Visceral leishmaniasis (VL), caused by the protozoan parasites and , is one of the major parasitic diseases worldwide. There is an urgent need for new drugs to treat VL, because current therapies are unfit for purpose in a resource-poor setting. Here, we describe the development of a preclinical drug candidate, GSK3494245/DDD01305143/compound 8, with potential to treat this neglected tropical disease. The compound series was discovered by repurposing hits from a screen against the related parasite Subsequent optimization of the chemical series resulted in the development of a potent cidal compound with activity against a range of clinically relevant and isolates. Compound 8 demonstrates promising pharmacokinetic properties and impressive in vivo efficacy in our mouse model of infection comparable with those of the current oral antileishmanial miltefosine. Detailed mode of action studies confirm that this compound acts principally by inhibition of the chymotrypsin-like activity catalyzed by the β5 subunit of the proteasome. High-resolution cryo-EM structures of apo and compound 8-bound 20S proteasome reveal a previously undiscovered inhibitor site that lies between the β4 and β5 proteasome subunits. This induced pocket exploits β4 residues that are divergent between humans and kinetoplastid parasites and is consistent with all of our experimental and mutagenesis data. As a result of these comprehensive studies and due to a favorable developability and safety profile, compound 8 is being advanced toward human clinical trials.
History
DepositionFeb 1, 2019-
Header (metadata) releaseApr 17, 2019-
Map releaseApr 17, 2019-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0667
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0667
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6qm7
  • Surface level: 0.0667
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4590.png

Downloads & links

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Map

FileDownload / File: emd_4590.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the sharpened EM map which was used for building the protein coordinates
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 300 pix.
= 321. Å		1.07 Å/pix.
x 300 pix.
= 321. Å		1.07 Å/pix.
x 300 pix.
= 321. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0667 / Movie #1: 0.0667
Minimum - Maximum-0.36080435 - 0.6223543
Average (Standard dev.)0.0010117632 (±0.022238906)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 321.00003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z321.000321.000321.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.3610.6220.001

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Supplemental data

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Sample components

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Entire : Proteasome 20S subunit

EntireName: Proteasome 20S subunit
Components
  • Complex: Proteasome 20S subunit
    • Protein or peptide: Proteasome alpha1 chain
    • Protein or peptide: Proteasome alpha2 chain
    • Protein or peptide: Proteasome alpha3 chain
    • Protein or peptide: Proteasome alpha4 chain
    • Protein or peptide: Proteasome alpha5 chain
    • Protein or peptide: Proteasome alpha6 chain
    • Protein or peptide: Proteasome alpha7 chain
    • Protein or peptide: Proteasome beta1 chain
    • Protein or peptide: Proteasome beta2 chain
    • Protein or peptide: Proteasome beta3 chain
    • Protein or peptide: Proteasome beta4 chain
    • Protein or peptide: Proteasome beta5 chain
    • Protein or peptide: Proteasome beta6 chain
    • Protein or peptide: Proteasome beta7 chain
  • Ligand: ~{N}-[4-fluoranyl-3-(3-morpholin-4-ylimidazo[1,2-a]pyrimidin-7-yl)phenyl]pyrrolidine-1-carboxamide
  • Ligand: water

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Supramolecule #1: Proteasome 20S subunit

SupramoleculeName: Proteasome 20S subunit / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#14
Source (natural)Organism: Leishmania tarentolae (eukaryote)

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Macromolecule #1: Proteasome alpha1 chain

MacromoleculeName: Proteasome alpha1 chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Molecular weightTheoretical: 27.178107 KDa
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 alpha2 chain

MacromoleculeName: Proteasome alpha2 chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Molecular weightTheoretical: 25.179559 KDa
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 alpha3 chain

MacromoleculeName: Proteasome alpha3 chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Molecular weightTheoretical: 32.321438 KDa
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 alpha4 chain

MacromoleculeName: Proteasome alpha4 chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Molecular weightTheoretical: 27.821605 KDa
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 alpha5 chain

MacromoleculeName: Proteasome alpha5 chain / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Molecular weightTheoretical: 38.312316 KDa
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 alpha6 chain

MacromoleculeName: Proteasome alpha6 chain / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Molecular weightTheoretical: 47.978633 KDa
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 alpha7 chain

MacromoleculeName: Proteasome alpha7 chain / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Molecular weightTheoretical: 25.591826 KDa
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 beta1 chain

MacromoleculeName: Proteasome beta1 chain / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Molecular weightTheoretical: 30.28001 KDa
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 beta2 chain

MacromoleculeName: Proteasome beta2 chain / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Molecular weightTheoretical: 27.60357 KDa
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 beta3 chain

MacromoleculeName: Proteasome beta3 chain / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Molecular weightTheoretical: 22.470887 KDa
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 beta4 chain

MacromoleculeName: Proteasome beta4 chain / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Molecular weightTheoretical: 23.065291 KDa
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 beta5 chain

MacromoleculeName: Proteasome beta5 chain / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Molecular weightTheoretical: 33.704867 KDa
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 beta6 chain

MacromoleculeName: Proteasome beta6 chain / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Molecular weightTheoretical: 37.67691 KDa
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 beta7 chain

MacromoleculeName: Proteasome beta7 chain / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Molecular weightTheoretical: 24.737232 KDa
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-(3-morpholin-4-ylimidazo[1,2-a]pyrimidin-7-yl...

MacromoleculeName: ~{N}-[4-fluoranyl-3-(3-morpholin-4-ylimidazo[1,2-a]pyrimidin-7-yl)phenyl]pyrrolidine-1-carboxamide
type: ligand / ID: 15 / Number of copies: 2 / Formula: J6E
Molecular weightTheoretical: 410.445 Da
Chemical component information

ChemComp-J6E:
~{N}-[4-fluoranyl-3-(3-morpholin-4-ylimidazo[1,2-a]pyrimidin-7-yl)phenyl]pyrrolidine-1-carboxamide

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Macromolecule #16: water

MacromoleculeName: water / type: ligand / ID: 16 / Number of copies: 334 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 182775
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

4r3o


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-6qm7:
Leishmania tarentolae proteasome 20S subunit complexed with GSK3494245

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