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- EMDB-15397: Symmetry expanded D7 local refined map of 20 proteasome protein f... -

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Basic information

Entry
Database: EMDB / ID: EMD-15397
TitleSymmetry expanded D7 local refined map of 20 proteasome protein from Chaetomium thermophilum
Map datacryo-EM 3D map of 20S proteasome from Chaetomium thermophilum. Local refined with D7 symmetry applied
Sample
  • Organelle or cellular component: native cell extract of Chaetomium thermophilum
    • Protein or peptide: x 14 types
Keywords20S Proteasome / Hydrolase / Chaetomium thermophilum / native cell extracts
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 / nucleus ...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 / 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 alpha6 / Proteasome subunit alpha5 / 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 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 / Putative proteasome protein / Proteasome subunit alpha type / Proteasome subunit alpha type / Proteasome alpha-type subunits domain-containing protein / Proteasome subunit beta / proteasome endopeptidase complex / Proteasome subunit alpha type / Proteasome alpha-type subunits domain-containing protein ...Proteasome subunit beta / Proteasome subunit beta / Putative proteasome protein / Proteasome subunit alpha type / Proteasome subunit alpha type / Proteasome alpha-type subunits domain-containing protein / Proteasome subunit beta / proteasome endopeptidase complex / Proteasome subunit alpha type / Proteasome alpha-type subunits domain-containing protein / Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit alpha type
Similarity search - Component
Biological speciesThermochaetoides thermophila DSM 1495 (fungus) / Thermochaetoides thermophila (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.74 Å
AuthorsSemchonok DA / Kyrilis FL / Hamdi F / Kastritis PL
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Symmetry expanded D7 local refined map of 20S proteasome from Chaetomium thermophilum
Authors: Semchonok DA / Kyrilis FL / Hamdi F / Kastritis PL
History
DepositionJul 17, 2022-
Header (metadata) releaseAug 16, 2023-
Map releaseAug 16, 2023-
UpdateAug 16, 2023-
Current statusAug 16, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15397.png

Downloads & links

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Map

FileDownload / File: emd_15397.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM 3D map of 20S proteasome from Chaetomium thermophilum. Local refined with D7 symmetry applied
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 256 pix.
= 245.76 Å		0.96 Å/pix.
x 256 pix.
= 245.76 Å		0.96 Å/pix.
x 256 pix.
= 245.76 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.422
Minimum - Maximum-0.9024796 - 1.4850488
Average (Standard dev.)0.011719574 (±0.10687204)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 245.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15397_msk_1.map
Projections & Slices
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Additional map: cryo-EM 3D map of 20S proteasome from Chaetomium...

Fileemd_15397_additional_1.map
Annotationcryo-EM 3D map of 20S proteasome from Chaetomium thermophilum with C1 symmetry
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: cryo-EM 3D mask for Hsp90 from Chaetomium thermophilum...

Fileemd_15397_additional_10.map
Annotationcryo-EM 3D mask for Hsp90 from Chaetomium thermophilum for C1 symmetry
Projections & Slices
AxesZYX

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Slices (1/2)
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Additional map: cryo-EM 3D map of Hsp60 from Chaetomium thermophilum...

Fileemd_15397_additional_11.map
Annotationcryo-EM 3D map of Hsp60 from Chaetomium thermophilum with local refinement and D7 symmetry applied
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: cryo-EM 3D mask for Hsp60 from Chaetomium thermophilum...

Fileemd_15397_additional_12.map
Annotationcryo-EM 3D mask for Hsp60 from Chaetomium thermophilum with local refinement and D7 symmetry applied
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: cryo-EM 3D map of Hsp60 from Chaetomium thermophilum with C1 symmetry

Fileemd_15397_additional_13.map
Annotationcryo-EM 3D map of Hsp60 from Chaetomium thermophilum with C1 symmetry
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: cryo-EM 3D mask for Hsp60 from Chaetomium thermophilum...

Fileemd_15397_additional_14.map
Annotationcryo-EM 3D mask for Hsp60 from Chaetomium thermophilum with C1 symmetry
Projections & Slices
AxesZYX

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Histogram (log scale)

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Additional map: cryo-EM 3D map of Hsp60 from Chaetomium thermophilum...

Fileemd_15397_additional_15.map
Annotationcryo-EM 3D map of Hsp60 from Chaetomium thermophilum with D7 symmetry applied
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: cryo-EM 3D mask for Hsp60 from Chaetomium thermophilum...

Fileemd_15397_additional_16.map
Annotationcryo-EM 3D mask for Hsp60 from Chaetomium thermophilum with D7 symmetry applied
Projections & Slices
AxesZYX

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Additional map: cryo-EM 3D map of UGPase from Chaetomium thermophilum...

Fileemd_15397_additional_17.map
Annotationcryo-EM 3D map of UGPase from Chaetomium thermophilum with C2 symmetry applied
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Additional map: cryo-EM 3D mask of 20S proteasome from Chaetomium...

Fileemd_15397_additional_2.map
Annotationcryo-EM 3D mask of 20S proteasome from Chaetomium thermophilum with C1 symmetry
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: cryo-EM 3D map of 20S proteasome from Chaetomium...

Fileemd_15397_additional_3.map
Annotationcryo-EM 3D map of 20S proteasome from Chaetomium thermophilum with D7 symmetry applied
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: cryo-EM 3D mask of 20S proteasome from Chaetomium...

Fileemd_15397_additional_4.map
Annotationcryo-EM 3D mask of 20S proteasome from Chaetomium thermophilum with D7 symmetry applied
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: cryo-EM 3D map of ACLY from Chaetomium thermophilum with C1 symmetry

Fileemd_15397_additional_5.map
Annotationcryo-EM 3D map of ACLY from Chaetomium thermophilum with C1 symmetry
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: cryo-EM 3D mask for ACLY from Chaetomium thermophilum...

Fileemd_15397_additional_6.map
Annotationcryo-EM 3D mask for ACLY from Chaetomium thermophilum with C1 symmetry
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: cryo-EM 3D map of ACLY from Chaetomium thermophilum...

Fileemd_15397_additional_7.map
Annotationcryo-EM 3D map of ACLY from Chaetomium thermophilum with D2 symmetry applied
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: cryo-EM 3D mask for ACLY from Chaetomium thermophilum...

Fileemd_15397_additional_8.map
Annotationcryo-EM 3D mask for ACLY from Chaetomium thermophilum with D2 symmetry applied
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: cryo-EM 3D map of Hsp90 from Chaetomium thermophilum with C1 symmetry

Fileemd_15397_additional_9.map
Annotationcryo-EM 3D map of Hsp90 from Chaetomium thermophilum with C1 symmetry
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_15397_half_map_1.map
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Half map: #1

Fileemd_15397_half_map_2.map
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Sample components

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Entire : native cell extract of Chaetomium thermophilum

EntireName: native cell extract of Chaetomium thermophilum
Components
  • Organelle or cellular component: native cell extract of Chaetomium thermophilum
    • Protein or peptide: Proteasome subunit alpha type-1
    • Protein or peptide: Proteasome subunit alpha type-2
    • Protein or peptide: Proteasome subunit alpha type-3
    • Protein or peptide: Proteasome subunit alpha type-4
    • Protein or peptide: Proteasome subunit alpha type-5
    • Protein or peptide: Proteasome subunit alpha type-6
    • Protein or peptide: Proteasome subunit alpha type-7
    • Protein or peptide: Proteasome subunit beta type-1
    • Protein or peptide: Proteasome subunit beta type-2
    • Protein or peptide: Proteasome subunit beta type-3
    • Protein or peptide: Proteasome subunit beta type-4
    • Protein or peptide: Proteasome subunit beta type-5
    • Protein or peptide: Proteasome subunit beta type-6
    • Protein or peptide: Proteasome subunit beta type-7

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Supramolecule #1: native cell extract of Chaetomium thermophilum

SupramoleculeName: native cell extract of Chaetomium thermophilum / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Purified and fractionated (fraction 25) cell lysate of Chaetomium thermophilum
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 600 KDa

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Macromolecule #1: Proteasome subunit alpha type-1

MacromoleculeName: Proteasome subunit alpha type-1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
SequenceString: MAGNAGYDRH ITIFSEQGRL YQVEYAFKAI TAANIMSIGV RGKDCAVVLS QKKVPDKLID PSSVTHIFQ ISPSIGCVIT GSIADARAWA QRAQSEAAEF KYKYGYEMPC DALAKRLANI S QVYTQRAY MRPYGIATTL IGMDEEFGPQ LFKCDPAGYY IGYKGTAAGP ...String:
MAGNAGYDRH ITIFSEQGRL YQVEYAFKAI TAANIMSIGV RGKDCAVVLS QKKVPDKLID PSSVTHIFQ ISPSIGCVIT GSIADARAWA QRAQSEAAEF KYKYGYEMPC DALAKRLANI S QVYTQRAY MRPYGIATTL IGMDEEFGPQ LFKCDPAGYY IGYKGTAAGP KQQEAINHLE KK LKNKDYA PGDWKEVVEL AITTLSTVLS MDFKKTEIEI GIVGGPRPDG KPGTYRGFRT LTE DEIDER LQAIAEKD

UniProtKB: Proteasome alpha-type subunits domain-containing protein

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Macromolecule #2: Proteasome subunit alpha type-2

MacromoleculeName: Proteasome subunit alpha type-2 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
SequenceString: MADRYSFSLT TFSPSGKLVQ IEYALNAVNQ GVTALGIKAT NGIVLATEKK SSTPLADPSS LSKISLITP NIGMVYAGMG PDYRVLVDRA RKVSHTNYKR IYNEYPPTRI LVQDVARVMQ E ATQSGGVR PYGVSLLIAG WDEGILPEEE EKTTEGQGTS TGEKKKAPGG ...String:
MADRYSFSLT TFSPSGKLVQ IEYALNAVNQ GVTALGIKAT NGIVLATEKK SSTPLADPSS LSKISLITP NIGMVYAGMG PDYRVLVDRA RKVSHTNYKR IYNEYPPTRI LVQDVARVMQ E ATQSGGVR PYGVSLLIAG WDEGILPEEE EKTTEGQGTS TGEKKKAPGG KTGGILKGGP ML YQVDPSG SYFPWKATAI GKSAATAKTF LEKRYTEGLE LEDAVHIALL TLKETIEGEM NGE TIEIGI VGPPADHLLG VEGVEGARGP RFRKLTPQEI EDYLTNL

UniProtKB: Proteasome subunit alpha type

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Macromolecule #3: Proteasome subunit alpha type-3

MacromoleculeName: Proteasome subunit alpha type-3 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
SequenceString: MARRYDSRTT IFSPDGRLYQ VEYALEAISH AGTAIGILAK DGIVLAAERK VTSKLLEQDT SAEKLYVIN DNMICAVAGM TADANILINF ARQVAQRYLL TYNEDIPCEQ LVRRLCDLKQ G YTQHGGLR PFGVSFIYAG WDPQREFQLY LSNPSGNYGG WKATSSGANH ...String:
MARRYDSRTT IFSPDGRLYQ VEYALEAISH AGTAIGILAK DGIVLAAERK VTSKLLEQDT SAEKLYVIN DNMICAVAGM TADANILINF ARQVAQRYLL TYNEDIPCEQ LVRRLCDLKQ G YTQHGGLR PFGVSFIYAG WDPQREFQLY LSNPSGNYGG WKATSSGANH ASAQSLLKQD YK EDCTLEE ACDLAVKVLS KTMDATKLSS DKIEFATVGK TKDGKIYHKL WSAEEITALL KKH DLAKDE TTEEK

UniProtKB: Proteasome subunit alpha type

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Macromolecule #4: Proteasome subunit alpha type-4

MacromoleculeName: Proteasome subunit alpha type-4 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
SequenceString: MASGYDRALS VFSPDGHVFQ VEYAGEAVKR GTCAVGVKGK DVVVLGCEKR SAMKLQDTRI TPSKIGLID SHVCLAFAGL NADARILIDK ARLEAQSHRL NLEDPVTIEY ITKYVAGVQQ R YTQSGGVR PFGISTLIVG FDKGSNVPRL YQTEPSGIYS AWKANAIGRS ...String:
MASGYDRALS VFSPDGHVFQ VEYAGEAVKR GTCAVGVKGK DVVVLGCEKR SAMKLQDTRI TPSKIGLID SHVCLAFAGL NADARILIDK ARLEAQSHRL NLEDPVTIEY ITKYVAGVQQ R YTQSGGVR PFGISTLIVG FDKGSNVPRL YQTEPSGIYS AWKANAIGRS SKTVREFLER NY KEDMDRE ATIRLAIKSL LEVVQTGAKN IEIAVMAPGK PMEMLPVEEI ENYVKSIEQE KQE EAAKKK TGRTPGTGTA TILTRPQDEP GDH

UniProtKB: Proteasome subunit alpha type

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Macromolecule #5: Proteasome subunit alpha type-5

MacromoleculeName: Proteasome subunit alpha type-5 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
SequenceString: MFVARSEYDR GINFTSSEIN PSPLANIPST FSPEGRLFQV EYSLEAIKLG STAIGVATSE GVILGVEKR VTSTLLETSS VEKIVEIDRH IGCAMSGLQA DARSMVEHAR VECQSHAFHY N EPLRVESC TQAICDLALR FGESADGEES IMSRPFGVAL LIAGIDEDGP ...String:
MFVARSEYDR GINFTSSEIN PSPLANIPST FSPEGRLFQV EYSLEAIKLG STAIGVATSE GVILGVEKR VTSTLLETSS VEKIVEIDRH IGCAMSGLQA DARSMVEHAR VECQSHAFHY N EPLRVESC TQAICDLALR FGESADGEES IMSRPFGVAL LIAGIDEDGP QLYHAEPSGT FY RYDAKAI GSGSEGAQAE LQNEYHKSLT LADAETLVLK TLKQVMEEKL DAKNVQLASV TKE RGFRIY TDEEMAAVVA RLPAN

UniProtKB: Proteasome alpha-type subunits domain-containing protein

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Macromolecule #6: Proteasome subunit alpha type-6

MacromoleculeName: Proteasome subunit alpha type-6 / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
SequenceString: MFRNNYDNDS VTFSPQGRIF QVEYAAEAVK QGSVVNPKPA QRRRTLVLPK KLFPIDEHVG IAIAGLTSD ARVLSNFMKQ QCLGHRLTYG RSMPVRTLVD LIGSKAQINT QHYGKRPYGV G LLIAGVDE HGPHLFEFQP SGMTEEMIAF AIGARSQMAR TYLEKHLDKF ...String:
MFRNNYDNDS VTFSPQGRIF QVEYAAEAVK QGSVVNPKPA QRRRTLVLPK KLFPIDEHVG IAIAGLTSD ARVLSNFMKQ QCLGHRLTYG RSMPVRTLVD LIGSKAQINT QHYGKRPYGV G LLIAGVDE HGPHLFEFQP SGMTEEMIAF AIGARSQMAR TYLEKHLDKF ADCSRDELIR HG LRALKES LVQDRELTID NTSVGVVGIK EQGEDGAAAK IEPFRVYDGQ DVAEWIESVS DER GAEGEG MEVDS

UniProtKB: Proteasome subunit alpha type

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Macromolecule #7: Proteasome subunit alpha type-7

MacromoleculeName: Proteasome subunit alpha type-7 / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
SequenceString: MTSIGTGYDL ANSIFSPDGR NFQVEYALKA VENGGTSIGI RCKEGVVLAV EKIITSKLLK PGANKRIAT VDRHIGIAFS GMIPDGRHFI DRARDEARAW RDTFKTPITT ADLASRMGGY M QAYTLYQS VRPFGITTII AGYDSPEDER VDGEVGRGPS CGAGGKVAGK ...String:
MTSIGTGYDL ANSIFSPDGR NFQVEYALKA VENGGTSIGI RCKEGVVLAV EKIITSKLLK PGANKRIAT VDRHIGIAFS GMIPDGRHFI DRARDEARAW RDTFKTPITT ADLASRMGGY M QAYTLYQS VRPFGITTII AGYDSPEDER VDGEVGRGPS CGAGGKVAGK THGGPYLYMI EP SGLYWGY YGAATGKGRQ AAKAELEKLD LQGDSLTLEQ AVKEAARIIY VAHDDSKDKD FEL EMTWIS GPDGPTKGLH QEVPKALREE AERLAKKALE DDDEEEAKEE KKDDDKMEE

UniProtKB: Proteasome subunit alpha type

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Macromolecule #8: Proteasome subunit beta type-1

MacromoleculeName: Proteasome subunit beta type-1 / type: protein_or_peptide / ID: 8 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
SequenceString: MEFGTTGCLS EDGIHLDMDR LKKGEVNLGT SIMAVTFKDG VILGADSRTT TGAYIANRVT DKLTQVHDT IWCCRSGSAA DTQAVADVVK YQLELFSMMN GRPPTTQTAA AIFQEICYAN K DMLSAGLI IAGWDPRHGG QVYSIPLGGS LHRQAYAIGG SGSTYIYGYC ...String:
MEFGTTGCLS EDGIHLDMDR LKKGEVNLGT SIMAVTFKDG VILGADSRTT TGAYIANRVT DKLTQVHDT IWCCRSGSAA DTQAVADVVK YQLELFSMMN GRPPTTQTAA AIFQEICYAN K DMLSAGLI IAGWDPRHGG QVYSIPLGGS LHRQAYAIGG SGSTYIYGYC DAHWREGMSE EE AVQFVKG ALREAIKWDG SSGGVIRMVV LTEKGAERHL YLPDTDYQVR HA

UniProtKB: Proteasome subunit beta

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Macromolecule #9: Proteasome subunit beta type-2

MacromoleculeName: Proteasome subunit beta type-2 / type: protein_or_peptide / ID: 9 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
SequenceString: MPGFDFSNYN RNVALHQRGV PLPKATSTGT TIVGCIYDGG VVIAADTRAT SGPIVADKNC EKLHYIAPN IWCAGAGTAA DTEFTTALIS SQIELHALST GRKPRVVTAM TMLKQHLFRY Q GYIGAYLV VAGVDPTGTH LFTVHAHGST DKLPYVTMGS GSLAAMAVFE ...String:
MPGFDFSNYN RNVALHQRGV PLPKATSTGT TIVGCIYDGG VVIAADTRAT SGPIVADKNC EKLHYIAPN IWCAGAGTAA DTEFTTALIS SQIELHALST GRKPRVVTAM TMLKQHLFRY Q GYIGAYLV VAGVDPTGTH LFTVHAHGST DKLPYVTMGS GSLAAMAVFE TQWKPSLTRE EA IKLCSDA IEAGIWNDLG SGSNVDVAVI TAEKTTLMRN YLKPNERTKK LGSYKFPKGT TAV LNEQVI KKEDITKYVT IHDLTEESGD KMEVDT

UniProtKB: proteasome endopeptidase complex

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Macromolecule #10: Proteasome subunit beta type-3

MacromoleculeName: Proteasome subunit beta type-3 / type: protein_or_peptide / ID: 10 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
SequenceString: MSSPFSINGG ACVAMVGKNC VAIACDLRLG LQALTVSNNF PKIFQYGDHV FLGLTGLATD VQTVADIFR YKVNLYRLRE ERHIAPRTFA NLVSSSLYER RFGPWFVSPV VAGLDPKTGE P FICGFDSI GCIDFAKDFI VSGTATEQLF GMCESLWEPD LGPEELFETI ...String:
MSSPFSINGG ACVAMVGKNC VAIACDLRLG LQALTVSNNF PKIFQYGDHV FLGLTGLATD VQTVADIFR YKVNLYRLRE ERHIAPRTFA NLVSSSLYER RFGPWFVSPV VAGLDPKTGE P FICGFDSI GCIDFAKDFI VSGTATEQLF GMCESLWEPD LGPEELFETI SQALLNAVDR DA LSGWGAH VYIIEKDKVT KRLLKGRQD

UniProtKB: Proteasome subunit beta

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Macromolecule #11: Proteasome subunit beta type-4

MacromoleculeName: Proteasome subunit beta type-4 / type: protein_or_peptide / ID: 11 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
SequenceString: MRGPTILKAT DDKTRQLNKH TLLAFSGEAG DTVQFAEYIQ ANSQLYSMRN ETDLSPAALA HFVRGELAS SLRSRHPYSV NLLLGGVDPI SGKPSLYWID YLASLAPVPY AAHGYAQYYC L SLLDKHHH PDIDLDQGRK LLDMCADELK RRLPIDFKGL VVKAVTKNGI ...String:
MRGPTILKAT DDKTRQLNKH TLLAFSGEAG DTVQFAEYIQ ANSQLYSMRN ETDLSPAALA HFVRGELAS SLRSRHPYSV NLLLGGVDPI SGKPSLYWID YLASLAPVPY AAHGYAQYYC L SLLDKHHH PDIDLDQGRK LLDMCADELK RRLPIDFKGL VVKAVTKNGI VDLPFDDDRI VK SANFVRA MGIGKHETDT LVDFNAGSSS QDVRCRKDVN YMQSRMLTNG TAGINGNADL AQQ KNLPQY KRTTPDFRVG

UniProtKB: Proteasome subunit beta

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Macromolecule #12: Proteasome subunit beta type-5

MacromoleculeName: Proteasome subunit beta type-5 / type: protein_or_peptide / ID: 12 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
SequenceString: MDKIVAQYSR PAYQQTELFD ELEQQDLVTT NPPLSLKFAM PPVTHPSAWL RAVTDDRSNP SCPIKIAHG TTTLAFRFKE GIIVATDSRA TAGNWIASQT VKKVIEINSE LLGTMAGGAA D CQYWLAWL GMQCRLHELR HKRRISVAAA SKILANLVYQ YKGMGLSMGT ...String:
MDKIVAQYSR PAYQQTELFD ELEQQDLVTT NPPLSLKFAM PPVTHPSAWL RAVTDDRSNP SCPIKIAHG TTTLAFRFKE GIIVATDSRA TAGNWIASQT VKKVIEINSE LLGTMAGGAA D CQYWLAWL GMQCRLHELR HKRRISVAAA SKILANLVYQ YKGMGLSMGT MCAGVTKEEG PA LYYIDSD GTRLAGNLFC VGSGQTFAYG VLDAEYRYDL TTEEALDLAS RSILAATHRD AYS GGYINL YHVKESGWVK HGFTDTNPVF WKTKLEKGEF SNVTSEF

UniProtKB: Proteasome subunit beta

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Macromolecule #13: Proteasome subunit beta type-6

MacromoleculeName: Proteasome subunit beta type-6 / type: protein_or_peptide / ID: 13 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
SequenceString: MAAMFSQNPL MNGPNYSFSD APRFSVPEGA REHRFDPYAD NGGSTLAIAG ADFTIMAGDT RLTSGYSIN SRYHPKLYKI GGTTADQSDA TIVLSVVGFA ADGEALKERL DAICKMYRYR H GKPMSVKA CAQRLSTILY QKRFFPYYAY AILGGLDEEG KGAVYSYDPV ...String:
MAAMFSQNPL MNGPNYSFSD APRFSVPEGA REHRFDPYAD NGGSTLAIAG ADFTIMAGDT RLTSGYSIN SRYHPKLYKI GGTTADQSDA TIVLSVVGFA ADGEALKERL DAICKMYRYR H GKPMSVKA CAQRLSTILY QKRFFPYYAY AILGGLDEEG KGAVYSYDPV GSYEREQCRA AG AAASLIM PFLDNQVNFK NQYVPGSGEG HNLQERPRRP LTRSEVEVLV KDAFDGAVER HIE VGDGLQ MMVITKDGIE EILLPLKRD

UniProtKB: Putative proteasome protein

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Macromolecule #14: Proteasome subunit beta type-7

MacromoleculeName: Proteasome subunit beta type-7 / type: protein_or_peptide / ID: 14 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
SequenceString: MDHRPQAWGR PRDDVFGPYD PSYLQTTGPK TATQQPIVTG TSVIAIKFKD GVVMAADNLA SYGSLARFT DVKRLHPFLG HTIVGFGGDV SDMQYLTRHL NELAIDEAYD HEAASAQSGG G SHLNAANL HKYLSKLMYR RRNSFDPLWN AILVAGFDSQ GKPFLGSVDL ...String:
MDHRPQAWGR PRDDVFGPYD PSYLQTTGPK TATQQPIVTG TSVIAIKFKD GVVMAADNLA SYGSLARFT DVKRLHPFLG HTIVGFGGDV SDMQYLTRHL NELAIDEAYD HEAASAQSGG G SHLNAANL HKYLSKLMYR RRNSFDPLWN AILVAGFDSQ GKPFLGSVDL RGTAFTSPSL AT GFGAMLA QPIMRKYAAT EGDTENMTRD EAVRVVKECM KVLFYRDARS LDRYSLAVVT KDG VELSED EQLEQQSWAF AERIRGYGTQ TVPSLSGSET ISALLALYP

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

Concentration0.3 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Pressure: 0.04 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Specialist opticsPhase plate: OTHER
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1109 / Average electron dose: 28.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 287314
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D7 (2x7 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 4433
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7ls5


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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