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- EMDB-15025: Leishmania tarentolae proteasome 20S subunit in complex with comp... -

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Basic information

Entry
Database: EMDB / ID: EMD-15025
TitleLeishmania tarentolae proteasome 20S subunit in complex with compound 2
Map datacoot contour level
Sample
  • Complex: Proteasome
    • Protein or peptide: x 14 types
  • Ligand: x 1 types
Function / homology
Function and homology information


proteasome core 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 / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / nucleus / cytoplasm
Similarity search - Function
Proteasome subunit alpha 1 / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit 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 beta 6 subunit, putative / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome alpha 5 subunit, putative / Proteasome subunit alpha type / Proteasome alpha 7 subunit, putative / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit beta ...Proteasome beta 6 subunit, putative / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome alpha 5 subunit, putative / Proteasome subunit alpha type / Proteasome alpha 7 subunit, putative / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit alpha type / Proteasome alpha 1 subunit, putative
Similarity search - Component
Biological speciesLeishmania tarentolae (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsSrinivas H
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Med Chem / Year: 2022
Title: Discovery of Novel Quinoline-Based Proteasome Inhibitors for Human African Trypanosomiasis (HAT).
Authors: Dennis C Koester / Vanessa M Marx / Sarah Williams / Jan Jiricek / Maxime Dauphinais / Olivier René / Sarah L Miller / Lei Zhang / Debjani Patra / Yen-Liang Chen / Harry Cheung / Jonathan ...Authors: Dennis C Koester / Vanessa M Marx / Sarah Williams / Jan Jiricek / Maxime Dauphinais / Olivier René / Sarah L Miller / Lei Zhang / Debjani Patra / Yen-Liang Chen / Harry Cheung / Jonathan Gable / Suresh B Lakshminarayana / Colin Osborne / Jean-Rene Galarneau / Upendra Kulkarni / Wendy Richmond / Angela Bretz / Linda Xiao / Frantisek Supek / Christian Wiesmann / Srinivas Honnappa / Celine Be / Pascal Mäser / Marcel Kaiser / Ryan Ritchie / Michael P Barrett / Thierry T Diagana / Christopher Sarko / Srinivasa P S Rao /
Abstract: Human African Trypanosomiasis (HAT) is a vector-borne disease caused by kinetoplastid parasites of the genus. The disease proceeds in two stages, with a hemolymphatic blood stage and a meningo- ...Human African Trypanosomiasis (HAT) is a vector-borne disease caused by kinetoplastid parasites of the genus. The disease proceeds in two stages, with a hemolymphatic blood stage and a meningo-encephalic brain stage. In the latter stage, the parasite causes irreversible damage to the brain leading to sleep cycle disruption and is fatal if untreated. An orally bioavailable treatment is highly desirable. In this study, we present a brain-penetrant, parasite-selective 20S proteasome inhibitor that was rapidly optimized from an HTS singleton hit to drug candidate compound that showed cure in a stage II mouse efficacy model. Here, we describe hit expansion and lead optimization campaign guided by cryo-electron microscopy and an model to predict the brain-to-plasma partition coefficient as an important parameter to prioritize compounds for synthesis. The model combined with in vitro and in vivo experiments allowed us to advance compounds with favorable unbound brain-to-plasma ratios () to cure a CNS disease such as HAT.
History
DepositionMay 24, 2022-
Header (metadata) releaseSep 28, 2022-
Map releaseSep 28, 2022-
UpdateSep 28, 2022-
Current statusSep 28, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15025.png

Downloads & links

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Map

FileDownload / File: emd_15025.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcoot contour level
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 300 pix.
= 258. Å		0.86 Å/pix.
x 300 pix.
= 258. Å		0.86 Å/pix.
x 300 pix.
= 258. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.8
Minimum - Maximum-3.3791552 - 9.885513
Average (Standard dev.)0.06926134 (±0.61104286)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 258.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: coot contour level

Fileemd_15025_additional_1.map
Annotationcoot contour level
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: coot contour level

Fileemd_15025_half_map_1.map
Annotationcoot contour level
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: coot contour level

Fileemd_15025_half_map_2.map
Annotationcoot contour level
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Proteasome

EntireName: Proteasome
Components
  • Complex: 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 subunit alpha type
    • Protein or peptide: Proteasome alpha 5 subunit, putative
    • Protein or peptide: Proteasome alpha 1 subunit, putative
    • Protein or peptide: Proteasome alpha 7 subunit, 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
    • Protein or peptide: Proteasome subunit beta
    • Protein or peptide: Proteasome beta 6 subunit, putative
    • Protein or peptide: Proteasome subunit beta
  • Ligand: ~{N}-cyclopentyl-6-methyl-4-phenylazanyl-quinoline-2-carboxamide

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Supramolecule #1: Proteasome

SupramoleculeName: Proteasome / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#14
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Molecular weightTheoretical: 840 KDa

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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
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 subunit alpha type

MacromoleculeName: Proteasome subunit alpha type / 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 subunit alpha type

MacromoleculeName: Proteasome subunit alpha type / 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 subunit alpha type

MacromoleculeName: Proteasome subunit alpha type / 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 alpha 5 subunit, putative

MacromoleculeName: Proteasome alpha 5 subunit, putative / 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 alpha 1 subunit, putative

MacromoleculeName: Proteasome alpha 1 subunit, putative / 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 alpha 7 subunit, putative

MacromoleculeName: Proteasome alpha 7 subunit, putative / 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 subunit beta

MacromoleculeName: Proteasome subunit beta / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Molecular weightTheoretical: 24.426352 KDa
SequenceString: TTILAVSYNG GVVLAADSRT SSGTYVVNRA SNKLTKLTKK IYCCRSGSAA DTQALAERVS NYLGSYQTDI GAGVNVATAA NLFQKMCYM NRWNISAGII VAGYDPINGG SVYSIPSGGS CVKLDYALGG SGSIFLYSFF DANYKPGMSK SECVAFCQRA V AHAYSRDG ...String:
TTILAVSYNG GVVLAADSRT SSGTYVVNRA SNKLTKLTKK IYCCRSGSAA DTQALAERVS NYLGSYQTDI GAGVNVATAA NLFQKMCYM NRWNISAGII VAGYDPINGG SVYSIPSGGS CVKLDYALGG SGSIFLYSFF DANYKPGMSK SECVAFCQRA V AHAYSRDG SSGGLIRTIT LDADEPEDQT IPWNRSPYCM EKDPKYVTQA TQNQPFSSSA KITGNRMSST G

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Macromolecule #9: Proteasome subunit beta

MacromoleculeName: Proteasome subunit beta / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Molecular weightTheoretical: 24.377994 KDa
SequenceString: TTIVGVVYRD GVVLGADTRA TEGSIVADKR CRKIHYMAPN IMCCGAGTSA DTEAVTNMVS SHLALHRLET GKQSRVLEAL TLLKRHLYR YQGHVSAALV LGGVDVEGPF LATIAPHGST DRLPFVTMGS GSIAAMAQLE AAYKDNMTCE EAKELVASAI R KGIFNDPY ...String:
TTIVGVVYRD GVVLGADTRA TEGSIVADKR CRKIHYMAPN IMCCGAGTSA DTEAVTNMVS SHLALHRLET GKQSRVLEAL TLLKRHLYR YQGHVSAALV LGGVDVEGPF LATIAPHGST DRLPFVTMGS GSIAAMAQLE AAYKDNMTCE EAKELVASAI R KGIFNDPY SGTQVDVCVI TKDKTELTIG YDKPNERMYP RQEVLLPPGT TPVLKEEIRQ 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
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 subunit beta

MacromoleculeName: Proteasome subunit beta / 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 subunit beta

MacromoleculeName: Proteasome subunit beta / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Molecular weightTheoretical: 22.56542 KDa
SequenceString: TTTLAFRFNG GIIVAVDSRA STGQYIASQT VMKVLEINDY LLGTLAGGAA DCQYWERVLG MECRLWELRN GSRITVAAAS KILANITYA YRNHGLSMGT MVAGWDQFGP SLYYVDDKGS RVKQDLFSVG SGSIYAYGVL DTGYRKDLSV EDACDLARRS I FHATYRDG ...String:
TTTLAFRFNG GIIVAVDSRA STGQYIASQT VMKVLEINDY LLGTLAGGAA DCQYWERVLG MECRLWELRN GSRITVAAAS KILANITYA YRNHGLSMGT MVAGWDQFGP SLYYVDDKGS RVKQDLFSVG SGSIYAYGVL DTGYRKDLSV EDACDLARRS I FHATYRDG ASGGIVTVYH VHEKGWTKIS RDDQTKLYHR YFPSQ

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Macromolecule #13: Proteasome beta 6 subunit, putative

MacromoleculeName: Proteasome beta 6 subunit, putative / 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 subunit beta

MacromoleculeName: Proteasome subunit beta / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Molecular weightTheoretical: 24.580037 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 I

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Macromolecule #15: ~{N}-cyclopentyl-6-methyl-4-phenylazanyl-quinoline-2-carboxamide

MacromoleculeName: ~{N}-cyclopentyl-6-methyl-4-phenylazanyl-quinoline-2-carboxamide
type: ligand / ID: 15 / Number of copies: 2 / Formula: KFC
Molecular weightTheoretical: 345.438 Da
Chemical component information

ChemComp-KFC:
~{N}-cyclopentyl-6-methyl-4-phenylazanyl-quinoline-2-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

Concentration2 mg/mL
BufferpH: 7
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 / Nominal defocus max: 20.0 µm / Nominal defocus min: 1.0 µm
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

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6tcz

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cisTEM (ver. 1.0)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 260000

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Jul 12, 2017. Major update of PDB

Major update of PDB

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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