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- EMDB-66543: Structure of the old Killifish Proteasome -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-66543
TitleStructure of the old Killifish Proteasome
Map dataSharpened old proteasome map
Sample
  • Complex: Structure of the old Killifish Proteasome
    • Protein or peptide: x 14 types
KeywordsProteasome / Nothobranchius furzeri / aging / skeletal muscle / HYDROLASE
Function / homology
Function and homology information


proteasome core complex / proteasome core complex, beta-subunit complex / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / protein catabolic process / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / nucleus / cytosol / cytoplasm
Similarity search - Function
Proteasome subunit alpha 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha5 / Proteasome subunit alpha6 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit ...Proteasome subunit alpha 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha5 / Proteasome subunit alpha6 / 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 B-type subunit / Proteasome beta-type subunit profile. / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit beta ...Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit alpha type / Proteasome subunit alpha type
Similarity search - Component
Biological speciesNothobranchius furzeri (turquoise killifish)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsKim J / Song JJ / Kim Y
Funding support Korea, Republic Of, 2 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)RS-2024-00333346 Korea, Republic Of
National Research Foundation (NRF, Korea)RS-2023-00266300 Korea, Republic Of
CitationJournal: To Be Published
Title: Ribosome remodels in age-dependent manner
Authors: Kim J / Hyeon DY / Lee S / Ryu BH / Gwak N / Choi Y / Vu HM / Huh S / Kim S / Myung K / Dieterich C / Valenzano DR / Kim MS / Hwang D / Song JJ / Kim Y
History
DepositionOct 10, 2025-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_66543.png

Downloads & links

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Map

FileDownload / File: emd_66543.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened old proteasome map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 331.2 Å		0.83 Å/pix.
x 400 pix.
= 331.2 Å		0.83 Å/pix.
x 400 pix.
= 331.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.045
Minimum - Maximum-0.20054919 - 0.36601642
Average (Standard dev.)0.0000091203365 (±0.012506663)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 331.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unfiltered old proteasome map

Fileemd_66543_additional_1.map
AnnotationUnfiltered old proteasome map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_66543_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66543_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of the old Killifish Proteasome

EntireName: Structure of the old Killifish Proteasome
Components
  • Complex: Structure of the old Killifish 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 subunit alpha type
    • Protein or peptide: Proteasome subunit alpha type
    • Protein or peptide: Proteasome subunit alpha type
    • Protein or peptide: Proteasome subunit beta
    • Protein or peptide: Proteasome subunit beta
    • Protein or peptide: Proteasome subunit beta
    • Protein or peptide: Proteasome subunit 5
    • Protein or peptide: Proteasome subunit beta
    • Protein or peptide: Proteasome subunit beta
    • Protein or peptide: Proteasome subunit beta

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Supramolecule #1: Structure of the old Killifish Proteasome

SupramoleculeName: Structure of the old Killifish Proteasome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Nothobranchius furzeri (turquoise killifish) / Tissue: skeletal muscle

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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: Nothobranchius furzeri (turquoise killifish) / Tissue: skeletal muscle
Molecular weightTheoretical: 25.900441 KDa
SequenceString: MAERGYSFSL TTFSPSGKLV QIEYALAAVA AGAPSVGIKA SNGVVLATEK KQKSILYDEQ SVHKVEPITK HIGMVYSGMG PDYRVLVRR ARKLAQQYYL VYQEPIPTGQ LVQRVASVMQ EYTQSGGVRP FGVSLLIAGW DEDHPYLFQS DPSGAYFAWK A TAMGKNYV ...String:
MAERGYSFSL TTFSPSGKLV QIEYALAAVA AGAPSVGIKA SNGVVLATEK KQKSILYDEQ SVHKVEPITK HIGMVYSGMG PDYRVLVRR ARKLAQQYYL VYQEPIPTGQ LVQRVASVMQ EYTQSGGVRP FGVSLLIAGW DEDHPYLFQS DPSGAYFAWK A TAMGKNYV NGKTFLEKRY NNDLELEDAI HTAILTLKES FEGQMTEENI EVGICNEAGF KRLTPAEVKD YLAAIA

UniProtKB: Proteasome subunit alpha type

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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: Nothobranchius furzeri (turquoise killifish) / Tissue: skeletal muscle
Molecular weightTheoretical: 29.405709 KDa
SequenceString: MSRRYDSRTT IFSPEGRLYQ VEYAMEAIGH AGTCLGILAN DGVLLAAERR NIHKLLDEVF FSEKIYKLNE DMACSVAGIT SDANVLTNE LRLIAQRYLL QYQEPIPCEQ LVTALCDIKQ AYTQFGGKRP FGVSLLYMGW DKHYGFQLYQ SDPSGNYGGW K ATCIGNNS ...String:
MSRRYDSRTT IFSPEGRLYQ VEYAMEAIGH AGTCLGILAN DGVLLAAERR NIHKLLDEVF FSEKIYKLNE DMACSVAGIT SDANVLTNE LRLIAQRYLL QYQEPIPCEQ LVTALCDIKQ AYTQFGGKRP FGVSLLYMGW DKHYGFQLYQ SDPSGNYGGW K ATCIGNNS AAAVSMLKQD YKEGEMTLSS ALALAIKVLN KTMDVSKLSA EKVEIATLTR EDGKTKIKVL KQKEVEELIK KH EAEEAKA EKDKKEKEQK EKDK

UniProtKB: Proteasome subunit alpha type

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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: Nothobranchius furzeri (turquoise killifish) / Tissue: skeletal muscle
Molecular weightTheoretical: 28.14323 KDa
SequenceString: MAARYDRAIT VFSPDGHLFQ VEYAQEAVKK GSTAVGIRGK DIVVLGVEKK SVAKLQEERT VRKICALDEH VCMAFAGLTA DARIVINRA RVECQSHRLT VEDPVTVEYI TRYIATLKQR YTQSNGRRPF GISALIVGFD YDGTPRLYQT DPSGTYHAWK A NAIGRSAK ...String:
MAARYDRAIT VFSPDGHLFQ VEYAQEAVKK GSTAVGIRGK DIVVLGVEKK SVAKLQEERT VRKICALDEH VCMAFAGLTA DARIVINRA RVECQSHRLT VEDPVTVEYI TRYIATLKQR YTQSNGRRPF GISALIVGFD YDGTPRLYQT DPSGTYHAWK A NAIGRSAK TVREFLEKNY TDEAIAGDNE AIKLAIKALL EVVQSGGKNI ELAVIRRNQP LKILESKEIE TLVAEIEKEK EE EAEKKKQ KKST

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: Nothobranchius furzeri (turquoise killifish) / Tissue: skeletal muscle
Molecular weightTheoretical: 26.44591 KDa
SequenceString: MFLTRSEYDR GVNTFSPEGR LFQVEYAIEA IKLGSTAIGI QTSEGVCLAV EKRITSPLME PNSIEKIVEI DSHIGCAMSG LIADAKTLI DKARVETQNH WFTYNETMTV ESVTQAVSNL ALQFGEEDAD PGAMSRPFGV ALLFGGVDEK GPQLYHMDPS G TFVQCDAR ...String:
MFLTRSEYDR GVNTFSPEGR LFQVEYAIEA IKLGSTAIGI QTSEGVCLAV EKRITSPLME PNSIEKIVEI DSHIGCAMSG LIADAKTLI DKARVETQNH WFTYNETMTV ESVTQAVSNL ALQFGEEDAD PGAMSRPFGV ALLFGGVDEK GPQLYHMDPS G TFVQCDAR AIGSASEGAQ SSLQEVYHKS MTLKDAIKSS LTILKQVMEE KLNATNIELA TVEPGKTFHM YSKEELEDVI KD I

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: Nothobranchius furzeri (turquoise killifish) / Tissue: skeletal muscle
Molecular weightTheoretical: 29.38042 KDa
SequenceString: MFRNQYDNDV TVWSPQGRIH QIEYAMEAVK QGSATVGLKS KTHAVLVALK RAQSELAAHQ KKILHVDNHI GISIAGLTAD ARLLCNFMR QECLDSRFVF DRPLPISRLV SLVGSKTQIP TQRYGRRPYG VGLLIAGFDD MGPHIFQTCP SANYFDCRAM S IGARSQSA ...String:
MFRNQYDNDV TVWSPQGRIH QIEYAMEAVK QGSATVGLKS KTHAVLVALK RAQSELAAHQ KKILHVDNHI GISIAGLTAD ARLLCNFMR QECLDSRFVF DRPLPISRLV SLVGSKTQIP TQRYGRRPYG VGLLIAGFDD MGPHIFQTCP SANYFDCRAM S IGARSQSA RTYLERLMDK FSDCNLNDLV QHGLRALRET LPAEQDLTTK NVSIGIVGKD MEFTIYDDDD VAPFLEGLEE RP QRKVAQP AVEPGAGEAP DEPMEH

UniProtKB: Proteasome subunit alpha type

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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
Source (natural)Organism: Nothobranchius furzeri (turquoise killifish) / Tissue: skeletal muscle
Molecular weightTheoretical: 28.428021 KDa
SequenceString: MSSIGTGYDL SASTFSPDGR VFQVEYAMKA VENSSTAIGI RCKDGVVFGV EKLVLSKLYE EGSNKRIFNI DKHVGMAVAG LLADARSLA DVAREEASSF RSNYGHNIPL KHLSDRVAMY AHAYTLYSAV RPFGCSFILG SYDKDDGSQL YMVDPSGISY G YWGCAIGK ...String:
MSSIGTGYDL SASTFSPDGR VFQVEYAMKA VENSSTAIGI RCKDGVVFGV EKLVLSKLYE EGSNKRIFNI DKHVGMAVAG LLADARSLA DVAREEASSF RSNYGHNIPL KHLSDRVAMY AHAYTLYSAV RPFGCSFILG SYDKDDGSQL YMVDPSGISY G YWGCAIGK AKQAAKTEIE KLQMKDMTCR ELVKEVAKII YIVHDEVKDK AFELELSWVG EVTNGRHEFV PKDIREEAEK YA KDSLEEE DDSDEDNM

UniProtKB: Proteasome subunit alpha type

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Macromolecule #7: Proteasome subunit alpha type

MacromoleculeName: Proteasome subunit alpha type / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Nothobranchius furzeri (turquoise killifish) / Tissue: skeletal muscle
Molecular weightTheoretical: 27.471342 KDa
SequenceString: MSRGSSAGFD RHITIFSPEG RLYQVEYAFK AINQGGLTSV AVRGKDCAVV VTQKKVPDKL LDASTVTHLF RITDTIGCVM SGMTADSRS QVQRARYEAA NWQYKYGYEI PVDMLCKRIA DVSQVYTQNA EMRPLGCCMI VIGVDEEFGP QVYKCDPAGY Y CGFKATAA ...String:
MSRGSSAGFD RHITIFSPEG RLYQVEYAFK AINQGGLTSV AVRGKDCAVV VTQKKVPDKL LDASTVTHLF RITDTIGCVM SGMTADSRS QVQRARYEAA NWQYKYGYEI PVDMLCKRIA DVSQVYTQNA EMRPLGCCMI VIGVDEEFGP QVYKCDPAGY Y CGFKATAA GVKQTEATSF LEKKVKKKLD WTFEQTVETA ISCLSTVLSI DFKPSELEVG VVTTQNPWFR TLTETEIDTH LM SLSERD

UniProtKB: Proteasome subunit alpha type

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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: Nothobranchius furzeri (turquoise killifish) / Tissue: skeletal muscle
Molecular weightTheoretical: 25.022373 KDa
SequenceString: MAATAAMMPN FGQQISSKND LVPDWTSQEV STGTTIMAVE YEGGVVIGAD SRTTTGAYIA NRVTDKLTPI HERIFCCRSG SAADTQAIA EVVSYQLGFH SIELDEPPLV ETAANLFRAS CYRYREELMA GILVAGWDRR KGGQVYCVPI GGMLVRQPVA V GGSGSSYI ...String:
MAATAAMMPN FGQQISSKND LVPDWTSQEV STGTTIMAVE YEGGVVIGAD SRTTTGAYIA NRVTDKLTPI HERIFCCRSG SAADTQAIA EVVSYQLGFH SIELDEPPLV ETAANLFRAS CYRYREELMA GILVAGWDRR KGGQVYCVPI GGMLVRQPVA V GGSGSSYI YGFMDSNYKP ALSKEECLEL TASALALAME RDGSSGGVIR LATISEAGVE RRVILGNQLP KFSTH

UniProtKB: Proteasome subunit beta

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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: Nothobranchius furzeri (turquoise killifish) / Tissue: skeletal muscle
Molecular weightTheoretical: 23.050857 KDa
SequenceString: MSIMSYNGGA VMAMRGKNCV AIAADRRFGI QAQMVTTDFQ KIFPMGDRLY IGLAGLATDV QTVAQRLKFR LNLYELKEGR QIKPKTFMS MVSNLLYERR FGPYYIEPVI AGLDPKSFEP FICSLDLIGC PMVTEDFVVS GTCSEQMYGM CESLWEPDME P EDLFETIS ...String:
MSIMSYNGGA VMAMRGKNCV AIAADRRFGI QAQMVTTDFQ KIFPMGDRLY IGLAGLATDV QTVAQRLKFR LNLYELKEGR QIKPKTFMS MVSNLLYERR FGPYYIEPVI AGLDPKSFEP FICSLDLIGC PMVTEDFVVS GTCSEQMYGM CESLWEPDME P EDLFETIS QAMLNAVDRD AVSGMGVVVH VIEKDKITTR TLKARMD

UniProtKB: Proteasome subunit beta

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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: Nothobranchius furzeri (turquoise killifish) / Tissue: skeletal muscle
Molecular weightTheoretical: 29.726891 KDa
SequenceString: MATVAVSRPP LGGFSFDNCK RNAILQGEAN KVGFNLPAAR KTGTTICGVV FKDGVVLGAD TRATEGMIVA DKNCSKIHYI SPNIYCCGA GTAADTEMTT QIISSNLELH ALSTGRLPRV ATANRMLKQM LFRYQGYIGA ALVLGGVDCN GPHLYSIYPH G STDKLPYV ...String:
MATVAVSRPP LGGFSFDNCK RNAILQGEAN KVGFNLPAAR KTGTTICGVV FKDGVVLGAD TRATEGMIVA DKNCSKIHYI SPNIYCCGA GTAADTEMTT QIISSNLELH ALSTGRLPRV ATANRMLKQM LFRYQGYIGA ALVLGGVDCN GPHLYSIYPH G STDKLPYV TMGSGSLAAM AVFEDRYKPN MEEGEAKQLV HDAIAAGIFN DLGSGSNIDL CVITKGSVDY IRPHDEANKK GV RTGDYKY RRGTTTVLTK AVNPLDLELV EESIQTMDTS

UniProtKB: Proteasome subunit beta

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Macromolecule #11: Proteasome subunit 5

MacromoleculeName: Proteasome subunit 5 / type: protein_or_peptide / ID: 11 / Details: Sequence refers to XP_054589013.1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Nothobranchius furzeri (turquoise killifish) / Tissue: skeletal muscle
Molecular weightTheoretical: 32.160512 KDa
SequenceString: MINPGRTAHA QRKLLVHHAL TKMALASVLS SDCVDFSFDY RQPFAVGCGP GQSGVDLEAA PGDSLKFSVK NSLLTGDEDG VERKIEFLH GTTTLAFKFQ HGVIVAVDSR ATAGSYIASQ TVKKVIEINP YLLGTMAGGA ADCSFWERLL ARQCRIYELR N KERISVAA ...String:
MINPGRTAHA QRKLLVHHAL TKMALASVLS SDCVDFSFDY RQPFAVGCGP GQSGVDLEAA PGDSLKFSVK NSLLTGDEDG VERKIEFLH GTTTLAFKFQ HGVIVAVDSR ATAGSYIASQ TVKKVIEINP YLLGTMAGGA ADCSFWERLL ARQCRIYELR N KERISVAA ASKLLANMVY QYKGMGLSMG TMVCGWDKRG PGLYYVDSEG NRVCGDLFAV GSGSMYAYGV VDSGVRNELT VE EACELGR RAIYQATYRD AYSGGQVNLY HVHSEGWTRV SQEDVLMLHQ RYKEQA

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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: Nothobranchius furzeri (turquoise killifish) / Tissue: skeletal muscle
Molecular weightTheoretical: 23.931572 KDa
SequenceString: MEYLIGIQGP DFVLVAADNV AASSIIQMKH DYDKMFKLSE KILLLCVGEA GDTVQFAEYI QKNVQLYKMR NGYELSPTAA ANFTRKNLA DYLRSRTPYH VNLLLAGYDE AEGPGLFYMD YLSSLAKAPF AAHGYGAFLT LSILDRYYRP DLSRDDAVDL L KKCVEELS ...String:
MEYLIGIQGP DFVLVAADNV AASSIIQMKH DYDKMFKLSE KILLLCVGEA GDTVQFAEYI QKNVQLYKMR NGYELSPTAA ANFTRKNLA DYLRSRTPYH VNLLLAGYDE AEGPGLFYMD YLSSLAKAPF AAHGYGAFLT LSILDRYYRP DLSRDDAVDL L KKCVEELS KRFILNLPSF TVRLIDKDGI HDMEKLTLSG EMARPMKATF YPAA

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: Nothobranchius furzeri (turquoise killifish) / Tissue: skeletal muscle
Molecular weightTheoretical: 28.307088 KDa
SequenceString: MESYGTKLSF WENGPKPGQF YSFPGSSTSC GPVRHTLNPM VTGTSVLGVK FKGGVVIAAD MLGSYGSLAR FRNISRLMKV NDNTILGAS GDYADYQYLK QVIEQMVIDE ELLGDGHSYS PKAIHSWLTR VMYNRRSKMN PLWNTVVIGG FYNGESFLGY V DKLGVAYE ...String:
MESYGTKLSF WENGPKPGQF YSFPGSSTSC GPVRHTLNPM VTGTSVLGVK FKGGVVIAAD MLGSYGSLAR FRNISRLMKV NDNTILGAS GDYADYQYLK QVIEQMVIDE ELLGDGHSYS PKAIHSWLTR VMYNRRSKMN PLWNTVVIGG FYNGESFLGY V DKLGVAYE APTVATGFGA YLAQPLMREV VENKAEITKQ EARDLVERCL KVLYYRDARS YNRHEIAIVT EEGVEIIGPL SS ETNWDIA HLISGFD

UniProtKB: Proteasome subunit beta

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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: Nothobranchius furzeri (turquoise killifish) / Tissue: skeletal muscle
Molecular weightTheoretical: 26.073697 KDa
SequenceString: MLSAQTFGDP GKMKDYHYTG PVEHRFSPYA FNGGTVLAVA GDDFAIVASD TRLSEGYSIH SRDSPKCYKL TDTTVIGCSG FHGDCLTLT KIIDARLKMY KHSNNKTMTS GAIAAMLSTI LYGRRFFPYY VYNIIGGLDE EGKGAVYSFD PVGSYQRDTY K AGGSASAM ...String:
MLSAQTFGDP GKMKDYHYTG PVEHRFSPYA FNGGTVLAVA GDDFAIVASD TRLSEGYSIH SRDSPKCYKL TDTTVIGCSG FHGDCLTLT KIIDARLKMY KHSNNKTMTS GAIAAMLSTI LYGRRFFPYY VYNIIGGLDE EGKGAVYSFD PVGSYQRDTY K AGGSASAM LQPLLDNQIG FKNMEGVQHV PLTKEKAVQL VKDVFISAAE RDVYTGDALR ICVITKKGID EQTLPLRKD

UniProtKB: Proteasome subunit beta

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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
Component:
ConcentrationFormulaName
100.0 mMKClPotassium Chloride
15.0 mMMgCl2Magnesium Chloride
20.0 mMTris-HClTris-hydrochloride
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV / Details: BioQuantum K3 Imaging filter
SoftwareName: EPU
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 9136 / Average exposure time: 5.87 sec. / Average electron dose: 60.23 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.3 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2953254
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 121745
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
FSC plot (resolution estimation)

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Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

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

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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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