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- EMDB-16901: CryoEM structure of 20S Trichomonas vaginalis proteasome in compl... -

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Basic information

Entry
Database: EMDB / ID: EMD-16901
TitleCryoEM structure of 20S Trichomonas vaginalis proteasome in complex with proteasome inhibitor Salinosporamid A
Map data2.89A CryoEM map of Tv20S proteasome with covalent inhibitor Salinosporamide A (Marizomib) bound to beta1 and beta2 subunits.
Sample
  • Complex: Ternary complex of 20S proteasome from Trichomonas vaginalis
    • Protein or peptide: x 14 types
  • Ligand: x 1 types
KeywordsProteasome / 20S / Trichomonas vaginalis / covalently bound Salinosporamide A / Marizomib / HYDROLASE
Function / homology
Function and homology information


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 / nucleus / cytosol / cytoplasm
Similarity search - Function
Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / 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 subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / 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
Family T1, proteasome alpha subunit, threonine peptidase / Proteasome subunit beta / Proteasome subunit alpha type / Family T1, proteasome alpha subunit, threonine peptidase / Proteasome subunit beta / proteasome endopeptidase complex / Proteasome subunit beta / Family T1, proteasome beta subunit, threonine peptidase / Family T1, proteasome alpha subunit, threonine peptidase / Proteasome subunit beta ...Family T1, proteasome alpha subunit, threonine peptidase / Proteasome subunit beta / Proteasome subunit alpha type / Family T1, proteasome alpha subunit, threonine peptidase / Proteasome subunit beta / proteasome endopeptidase complex / Proteasome subunit beta / Family T1, proteasome beta subunit, threonine peptidase / Family T1, proteasome alpha subunit, threonine peptidase / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit alpha type / Family T1, proteasome alpha subunit, threonine peptidase / Proteasome subunit alpha type
Similarity search - Component
Biological speciesTrichomonas vaginalis G3 (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsSilhan J / Fajtova P / Boura E
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission846688European Union
CitationJournal: To Be Published
Title: Tv20S proteasome in the complex with marizomib
Authors: Silhan J / Fajtova P / O'Donoghue A / Boura E
History
DepositionMar 23, 2023-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateApr 17, 2024-
Current statusApr 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16901.png

Downloads & links

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Map

FileDownload / File: emd_16901.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation2.89A CryoEM map of Tv20S proteasome with covalent inhibitor Salinosporamide A (Marizomib) bound to beta1 and beta2 subunits.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.7 Å/pix.
x 440 pix.
= 308. Å		0.7 Å/pix.
x 440 pix.
= 308. Å		0.7 Å/pix.
x 440 pix.
= 308. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.133
Minimum - Maximum-0.47978264 - 0.8276519
Average (Standard dev.)0.000611609 (±0.03965521)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 308.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: 2.89A CryoEM map of Tv20S proteasome with covalent...

Fileemd_16901_half_map_1.map
Annotation2.89A CryoEM map of Tv20S proteasome with covalent inhibitor Salinosporamide A (Marizomib) bound to beta1 and beta2 subunits.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 2.89A CryoEM map of Tv20S proteasome with covalent...

Fileemd_16901_half_map_2.map
Annotation2.89A CryoEM map of Tv20S proteasome with covalent inhibitor Salinosporamide A (Marizomib) bound to beta1 and beta2 subunits.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of 20S proteasome from Trichomonas vaginalis

EntireName: Ternary complex of 20S proteasome from Trichomonas vaginalis
Components
  • Complex: Ternary complex of 20S proteasome from Trichomonas vaginalis
    • Protein or peptide: Family T1, proteasome alpha subunit, threonine peptidase
    • Protein or peptide: Family T1, proteasome alpha subunit, threonine peptidase
    • Protein or peptide: Proteasome subunit alpha type
    • Protein or peptide: Proteasome subunit alpha type
    • Protein or peptide: Proteasome subunit alpha type
    • Protein or peptide: Family T1, proteasome alpha subunit, threonine peptidase
    • Protein or peptide: Family T1, proteasome alpha subunit, threonine peptidase
    • Protein or peptide: Proteasome subunit beta
    • 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 beta
    • Protein or peptide: Family T1, proteasome beta subunit, threonine peptidase
  • Ligand: (3AR,6R,6AS)-6-((S)-((S)-CYCLOHEX-2-ENYL)(HYDROXY)METHYL)-6A-METHYL-4-OXO-HEXAHYDRO-2H-FURO[3,2-C]PYRROLE-6-CARBALDEHYDE

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Supramolecule #1: Ternary complex of 20S proteasome from Trichomonas vaginalis

SupramoleculeName: Ternary complex of 20S proteasome from Trichomonas vaginalis
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#14
Details: Subunits beta 1 and beta 2 a covalently attached to protease inhibitor marizomib (Salinosporamid A)
Source (natural)Organism: Trichomonas vaginalis G3 (eukaryote)
Molecular weightTheoretical: 704 KDa

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Macromolecule #1: Family T1, proteasome alpha subunit, threonine peptidase

MacromoleculeName: Family T1, proteasome alpha subunit, threonine peptidase
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Trichomonas vaginalis G3 (eukaryote)
Molecular weightTheoretical: 26.511184 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSSGADRYLT VFSAEGRLWQ VEYSFKAVKQ AEVTAVAVKS KNAVCVAVQK KVSDKLIDPS TVTHMYRITD NVGACLVGLP SDVNFIVML LRSFANNFEY KQGFSIPVSI LAQMLSERHQ LESQLVYVRP SAVSAILFGL DGPSDSFALY KIEPSGYSNG F RAVACGVK ...String:
MSSGADRYLT VFSAEGRLWQ VEYSFKAVKQ AEVTAVAVKS KNAVCVAVQK KVSDKLIDPS TVTHMYRITD NVGACLVGLP SDVNFIVML LRSFANNFEY KQGFSIPVSI LAQMLSERHQ LESQLVYVRP SAVSAILFGL DGPSDSFALY KIEPSGYSNG F RAVACGVK EIEAMSALEK KMEDFETPEA TAEFTLSTLQ TVCGVDFEAQ DVEVSLLTRD NSKFSKLPND KVNEILHAVA EK D

UniProtKB: Family T1, proteasome alpha subunit, threonine peptidase

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Macromolecule #2: Family T1, proteasome alpha subunit, threonine peptidase

MacromoleculeName: Family T1, proteasome alpha subunit, threonine peptidase
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Trichomonas vaginalis G3 (eukaryote)
Molecular weightTheoretical: 25.444994 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGDSDFSLTT FSSGGKLNQI ESALKAVSLG GQCVGVKAKN GAVIACESKP SSPLVEKVTN LKVQKINDNV GIVYSGVNTD FHVILKSLR KASIKYSLRL GVEMPTREVV KHAAHKMQYY TQIGGVRPFG VSLLIIGWEE LGPTLWQVDP SGTFWAWKAT A LGKRSDGS ...String:
MGDSDFSLTT FSSGGKLNQI ESALKAVSLG GQCVGVKAKN GAVIACESKP SSPLVEKVTN LKVQKINDNV GIVYSGVNTD FHVILKSLR KASIKYSLRL GVEMPTREVV KHAAHKMQYY TQIGGVRPFG VSLLIIGWEE LGPTLWQVDP SGTFWAWKAT A LGKRSDGS RTFLERRYSE DQSVDDAIHT AISTLKEGFD GQLTAELIEI GVVDETRKFR TLSTAEIRDF LTEV

UniProtKB: Family T1, proteasome alpha subunit, threonine peptidase

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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: Trichomonas vaginalis G3 (eukaryote)
Molecular weightTheoretical: 27.989707 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MTYRYDAGTT TFSSDGRILQ VEYAIQSINQ AGTAIGVQFT NGVVLAAEKK NTGRLVDYLF PEKMAKIDGH IVTAVAGLTA DANTLVDLM RTSAQKYLKT YDEQMPVEQL VRMVCDEKHS YTQYGGLRPY GVSFLIAGYD RHKGCQLYLT DPSGNFGGWK A TAIGENNQ ...String:
MTYRYDAGTT TFSSDGRILQ VEYAIQSINQ AGTAIGVQFT NGVVLAAEKK NTGRLVDYLF PEKMAKIDGH IVTAVAGLTA DANTLVDLM RTSAQKYLKT YDEQMPVEQL VRMVCDEKHS YTQYGGLRPY GVSFLIAGYD RHKGCQLYLT DPSGNFGGWK A TAIGENNQ TAQSILKSQY KDNMTATEAM DLTVKVLCKT LDSTSLSADK LEFAVLQFRE EYGPKVRILT TSEVDTLMKR YE ETIKKSA EEKE

UniProtKB: Proteasome subunit alpha type

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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: Trichomonas vaginalis G3 (eukaryote)
Molecular weightTheoretical: 26.306916 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSDYTRSITR FSPDGRLFQI DHAHAAVQRG TTVVATRSKD MIVIAVEKTA VAKLQDPHTF SKICSLDKHV MCAFAGLHAD ARRLIQSGQ RQCQSHRLTY EDPISIENIA RYIATLQLKN TQSGGARPYG VSTLICGFDD MTSQPHIYET LPSGTYAEWK A RTIGRHDQ ...String:
MSDYTRSITR FSPDGRLFQI DHAHAAVQRG TTVVATRSKD MIVIAVEKTA VAKLQDPHTF SKICSLDKHV MCAFAGLHAD ARRLIQSGQ RQCQSHRLTY EDPISIENIA RYIATLQLKN TQSGGARPYG VSTLICGFDD MTSQPHIYET LPSGTYAEWK A RTIGRHDQ TVMEYLEKHY KDDMTDEEAQ KLAIGALLEV VENGSKNLEV AYMKRGGTME IMAEEVLDAL IESTKAK

UniProtKB: Proteasome subunit alpha type

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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
Source (natural)Organism: Trichomonas vaginalis G3 (eukaryote)
Molecular weightTheoretical: 27.330986 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MFNSGSEYDR NVNTFSPDGR LLQVEYAIEA VKLGSSAVAI LCPEGVIFAV EKRLSSQLLI ASSVEKVYAI DDHVGVVMAG LAADGRTMV EHMRVEAQNH RFSFDEPIGI KAVTQSVCDL ALAFGEGRRK KGDGQMSRPF GTALLVAGIE NGKCHLFHTD P SGTYTECR ...String:
MFNSGSEYDR NVNTFSPDGR LLQVEYAIEA VKLGSSAVAI LCPEGVIFAV EKRLSSQLLI ASSVEKVYAI DDHVGVVMAG LAADGRTMV EHMRVEAQNH RFSFDEPIGI KAVTQSVCDL ALAFGEGRRK KGDGQMSRPF GTALLVAGIE NGKCHLFHTD P SGTYTECR ARAIGGGSEG AEALLRDLYK DGMTLHEAED LALSTLRQVI QEKLNENNVE VACARVSTGK FEIYTSEQRQ EI VARLPPP IIPE

UniProtKB: Proteasome subunit alpha type

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Macromolecule #6: Family T1, proteasome alpha subunit, threonine peptidase

MacromoleculeName: Family T1, proteasome alpha subunit, threonine peptidase
type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Trichomonas vaginalis G3 (eukaryote)
Molecular weightTheoretical: 25.682287 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MFRSKYDENA TTFSPEGRIL QVENAMKAVQ QGMPTVGLKS KTHAVIAGVM HSPSEFSSHQ PKIFKIDQHI GVAISGLTAD GRGLCKFLR NECLHHTFCF GTEIRVADLA DTVALQSQKK TSKVGKRPYG VGLLMIGAGV DGPRLFETCP SGQHWEYNAQ A IGRRAQAA ...String:
MFRSKYDENA TTFSPEGRIL QVENAMKAVQ QGMPTVGLKS KTHAVIAGVM HSPSEFSSHQ PKIFKIDQHI GVAISGLTAD GRGLCKFLR NECLHHTFCF GTEIRVADLA DTVALQSQKK TSKVGKRPYG VGLLMIGAGV DGPRLFETCP SGQHWEYNAQ A IGRRAQAA KTYLETNLNE FPDCTRDQLI RHALRALNDC KSRESDSLEA IALGVVGIDE PFTILEGPEL QKYID

UniProtKB: Family T1, proteasome alpha subunit, threonine peptidase

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Macromolecule #7: Family T1, proteasome alpha subunit, threonine peptidase

MacromoleculeName: Family T1, proteasome alpha subunit, threonine peptidase
type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Trichomonas vaginalis G3 (eukaryote)
Molecular weightTheoretical: 27.067422 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSGAGSGYDF NPITFSPDGR QFQVEYATKA VEKDSLALGV KCKDGILLAA EKNLTSTLLT PGGNPRIFWI NDSIACATIG HRPDCYSIV EQSRNRAETF TSNFGIKITV PQLASEVSQQ FHLAHYYQAY RPFGCTVIFA SYKDDALYAI EPSGAFYGYF A SCFGKNSN ...String:
MSGAGSGYDF NPITFSPDGR QFQVEYATKA VEKDSLALGV KCKDGILLAA EKNLTSTLLT PGGNPRIFWI NDSIACATIG HRPDCYSIV EQSRNRAETF TSNFGIKITV PQLASEVSQQ FHLAHYYQAY RPFGCTVIFA SYKDDALYAI EPSGAFYGYF A SCFGKNSN LARAELQKTE WKNITVREAV PEVARIIKSL HESQFKKWEI EMFWLCEETN GRPQKVPEDV FQSRFVNENP QN

UniProtKB: Family T1, proteasome alpha subunit, threonine peptidase

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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: Trichomonas vaginalis G3 (eukaryote)
Molecular weightTheoretical: 21.930805 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: TTLLAIQCTD GVVMASDSRT SSGSFIPNRA TNKITEIQPK IFAARCGNAA DTQFLARAVK NYLNALNITR ENTDDSTILV ASNVIRSLI VRYRQYLSAG VIVGGWDSAG PQVYSIEVSG MAIKKKIASN GSGSTYIQAY IDQNYREDMT MEEATKFAIA A VTGAIIRD ...String:
TTLLAIQCTD GVVMASDSRT SSGSFIPNRA TNKITEIQPK IFAARCGNAA DTQFLARAVK NYLNALNITR ENTDDSTILV ASNVIRSLI VRYRQYLSAG VIVGGWDSAG PQVYSIEVSG MAIKKKIASN GSGSTYIQAY IDQNYREDMT MEEATKFAIA A VTGAIIRD GSSGGVVNIV QINADGAKRM TVRPAQQPFN YDIVKG

UniProtKB: Proteasome subunit beta

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Macromolecule #9: proteasome endopeptidase complex

MacromoleculeName: proteasome endopeptidase complex / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Trichomonas vaginalis G3 (eukaryote)
Molecular weightTheoretical: 26.869426 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: TTIAAAIFDG GVVLGADTRA TAGPIVAVKD EMKLHYISDN IWVCGAGIAA DNDNINAVIS AKLRLFQMNT GLQPRVDQCT NILASRLFQ YMGYIQAALI VGGIDFQGPQ VYQVAPHGSF SKQPFIAQGS GSLAAISVLE NRWHNKMNEH DCMEMVADAI Y AGITNDLG ...String:
TTIAAAIFDG GVVLGADTRA TAGPIVAVKD EMKLHYISDN IWVCGAGIAA DNDNINAVIS AKLRLFQMNT GLQPRVDQCT NILASRLFQ YMGYIQAALI VGGIDFQGPQ VYQVAPHGSF SKQPFIAQGS GSLAAISVLE NRWHNKMNEH DCMEMVADAI Y AGITNDLG SGSHVNLCVI KRENPEDKQS KVIYTFYKDY RVPHENDRNF RLEPQINNID VEVIKTTERP LTLPDVHLEI LD DAPA

UniProtKB: proteasome endopeptidase complex

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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: Trichomonas vaginalis G3 (eukaryote)
Molecular weightTheoretical: 23.028574 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSDISTYNGS CVLAMAGDHC VAIASDRRLG VNMLTVSKDF KRIFQINDRI YLGLAGLATD VLTVREQLRF DVNLLELREE RPIDPKKFM NLVKSTLYEK RFSPFFVTPV IAGLLPETNE PYLAASDSIG AFAFPKDFAV AGTCEESLYG ICESAWRPNM N PDELFECT ...String:
MSDISTYNGS CVLAMAGDHC VAIASDRRLG VNMLTVSKDF KRIFQINDRI YLGLAGLATD VLTVREQLRF DVNLLELREE RPIDPKKFM NLVKSTLYEK RFSPFFVTPV IAGLLPETNE PYLAASDSIG AFAFPKDFAV AGTCEESLYG ICESAWRPNM N PDELFECT AKCLIAAVER DSISGWGGIV YIITQDKVII KEIKTRMD

UniProtKB: Proteasome subunit beta

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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: Trichomonas vaginalis G3 (eukaryote)
Molecular weightTheoretical: 21.4216 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MLSIVGLQGP DWVLIAADSS VSSSIICMSE NYDRIAQLDD RHALAMSGET GDCLQLSEYL QGNVALYKFR NGVELSSDAL AHFIRHTMA KAVRKSPYEV NMLLSGYDGK PHLYFMDYLG TLQSIPYGAQ GYCQYFVMSV FDKHYKEGLT LEDGKELMKL A LNQIKQRF TVAPHGFIVK LVDKNGITKI DLE

UniProtKB: Proteasome subunit beta

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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: Trichomonas vaginalis G3 (eukaryote)
Molecular weightTheoretical: 22.572598 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: TTTLSFIYNG GIVVAVDSRA TGGQFIFSQT VMKILPLAPN MIGTMAGGAA DCQYWLRNLS RLIQLHKFRY QQPLTVAAAS KILVNELYR YKGYNLSIGS MICGYDNTGP HIFYIDNHGS RIAGKRFSVG SGSTHAYGVL DTCYREDMTK EEACELGRRA I YHATYRDS ...String:
TTTLSFIYNG GIVVAVDSRA TGGQFIFSQT VMKILPLAPN MIGTMAGGAA DCQYWLRNLS RLIQLHKFRY QQPLTVAAAS KILVNELYR YKGYNLSIGS MICGYDNTGP HIFYIDNHGS RIAGKRFSVG SGSTHAYGVL DTCYREDMTK EEACELGRRA I YHATYRDS GSGGRVSVVH ITQNGVEWID KTDVFDMHDF SKTTF

UniProtKB: Proteasome subunit beta

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Macromolecule #13: Proteasome subunit beta

MacromoleculeName: Proteasome subunit beta / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Trichomonas vaginalis G3 (eukaryote)
Molecular weightTheoretical: 25.001025 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEGEFRENKK GQWSPYEMHG GTAIGICGDD YVVIGADTRL SVDYSIDSRH KARIFKMNSN CMISATGFDG DIDAFITRMR SILLNYENQ HFHEMSVESV ARCVSNTLYS KRFFPYYINI LVGGINSEGK GKLYGYDPVG TIEDLHYDSN GSGSSLAAPL L DSAFGTIH ...String:
MEGEFRENKK GQWSPYEMHG GTAIGICGDD YVVIGADTRL SVDYSIDSRH KARIFKMNSN CMISATGFDG DIDAFITRMR SILLNYENQ HFHEMSVESV ARCVSNTLYS KRFFPYYINI LVGGINSEGK GKLYGYDPVG TIEDLHYDSN GSGSSLAAPL L DSAFGTIH HNTRPFPAVS LQDAKNIVRD AICSVTERDI YTGDALQLCV FTKDGFAQEE FPLPRH

UniProtKB: Proteasome subunit beta

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Macromolecule #14: Family T1, proteasome beta subunit, threonine peptidase

MacromoleculeName: Family T1, proteasome beta subunit, threonine peptidase
type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Trichomonas vaginalis G3 (eukaryote)
Molecular weightTheoretical: 26.486643 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MQVITASGAI VAAKYDGGIL LASDLSITYG SMFRHNNVSH FVEVAPNIII GASGEFADFQ TLIEVIKSVI LQQQCKHNGE YLTASEVHN YIKRYMYQCR SNMKPLSCKV IVAGINPDGS KFLACTDPYG ASWESDHIGT GFGKYLQGLQ IADVVNGSFD D VKKGITEV ...String:
MQVITASGAI VAAKYDGGIL LASDLSITYG SMFRHNNVSH FVEVAPNIII GASGEFADFQ TLIEVIKSVI LQQQCKHNGE YLTASEVHN YIKRYMYQCR SNMKPLSCKV IVAGINPDGS KFLACTDPYG ASWESDHIGT GFGKYLQGLQ IADVVNGSFD D VKKGITEV FRAVNARNTT ANGKIEFITV TPQGINHLAP EQIDPNWEVV EGTWDQSAWS HPQFEKGGGS GGGSGGSAWS HP QFEK

UniProtKB: Family T1, proteasome beta subunit, threonine peptidase

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Macromolecule #15: (3AR,6R,6AS)-6-((S)-((S)-CYCLOHEX-2-ENYL)(HYDROXY)METHYL)-6A-METH...

MacromoleculeName: (3AR,6R,6AS)-6-((S)-((S)-CYCLOHEX-2-ENYL)(HYDROXY)METHYL)-6A-METHYL-4-OXO-HEXAHYDRO-2H-FURO[3,2-C]PYRROLE-6-CARBALDEHYDE
type: ligand / ID: 15 / Number of copies: 4 / Formula: SA1
Molecular weightTheoretical: 279.332 Da
Chemical component information

ChemComp-SA1:
(3AR,6R,6AS)-6-((S)-((S)-CYCLOHEX-2-ENYL)(HYDROXY)METHYL)-6A-METHYL-4-OXO-HEXAHYDRO-2H-FURO[3,2-C]PYRROLE-6-CARBALDEHYDE

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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

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMHEPESHEPES
150.0 mMNaClSodium chloridesodium chloride
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.015 kPa / Details: 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.6 µm / Nominal defocus min: 0.8 µm
Specialist opticsEnergy filter - Name: TFS Selectris
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 7983 / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2303719
Startup modelType of model: INSILICO MODEL
In silico model: a startup model was generated using AlphaFold predicted monomers that were superimposed onto 20S PDB:7ZYJ
Details: 7ZYJ LEISHMANIA TARENTOLAE PROTEASOME 20S SUBUNIT IN COMPLEX WITH COMPOUND was used as a template for the superimposition of all 14 AlphaFold-generated models.
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: OTHER
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Details: Standard Homo Refine job in Cryosparc v4 / Number images used: 14257
FSC plot (resolution estimation)

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