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- EMDB-14175: Spinach 26S proteasome -

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Basic information

Entry
Database: EMDB / ID: EMD-14175
TitleSpinach 26S proteasome
Map data
Sample
  • Complex: Spinach 26S proteasome
    • Protein or peptide: x 14 types
KeywordsPROTEASOME / UPS / PLANT / SPINACH / PLANT PROTEIN
Function / homology
Function and homology information


: / : / nuclear proteasome complex / cytosolic proteasome complex / proteasome regulatory particle / proteasome regulatory particle, lid subcomplex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / metal-dependent deubiquitinase activity / proteasome core complex ...: / : / nuclear proteasome complex / cytosolic proteasome complex / proteasome regulatory particle / proteasome regulatory particle, lid subcomplex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / metal-dependent deubiquitinase activity / proteasome core complex / K63-linked deubiquitinase activity / proteasome binding / regulation of protein catabolic process / proteasome storage granule / polyubiquitin modification-dependent protein binding / positive regulation of RNA polymerase II transcription preinitiation complex assembly / protein deubiquitination / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / membrane => GO:0016020 / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / enzyme regulator activity / proteasome complex / proteolysis involved in protein catabolic process / metallopeptidase activity / peptidase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / structural molecule activity / ATP hydrolysis activity / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Proteasome subunit alpha2 / Proteasome subunit alpha4 / 26S Proteasome non-ATPase regulatory subunit 14 / 26S proteasome regulatory subunit P45-like / 26S Proteasome regulatory subunit 6B / 26S proteasome regulatory subunit 8 / Ubiquitin interaction motif / 26S proteasome non-ATPase regulatory subunit Rpn12 / 26S proteasome regulatory subunit, C-terminal / Proteasome regulatory subunit C-terminal ...Proteasome subunit alpha2 / Proteasome subunit alpha4 / 26S Proteasome non-ATPase regulatory subunit 14 / 26S proteasome regulatory subunit P45-like / 26S Proteasome regulatory subunit 6B / 26S proteasome regulatory subunit 8 / Ubiquitin interaction motif / 26S proteasome non-ATPase regulatory subunit Rpn12 / 26S proteasome regulatory subunit, C-terminal / Proteasome regulatory subunit C-terminal / 26S proteasome regulatory subunit RPN5, C-terminal domain / 26S proteasome regulatory subunit RPN5 C-terminal domain / 26S proteasome regulatory subunit Rpn6, N-terminal / 6S proteasome subunit Rpn6, C-terminal helix domain / 26S proteasome regulatory subunit RPN6 N-terminal domain / 26S proteasome subunit RPN6 C-terminal helix domain / 26S Proteasome non-ATPase regulatory subunit 13 / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / 26S proteasome regulatory subunit RPN2, C-terminal / 26S proteasome regulatory subunit RPN2 C-terminal domain / 26S Proteasome non-ATPase regulatory subunit 7/8 / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / RPN1, N-terminal / 26S proteasome non-ATPase regulatory subunit RPN1, C-terminal / RPN1 N-terminal domain / 26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / : / 26S proteasome regulatory subunit 7, OB domain / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 26S proteasome regulatory subunit Rpn7, N-terminal / 26S proteasome subunit RPN7 / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / Proteasome/cyclosome repeat / Proteasome/cyclosome repeat / Ubiquitin-interacting motif. / : / von Willebrand factor type A domain / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / Proteasome subunit alpha 1 / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / 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 / von Willebrand factor (vWF) type A domain / VWFA domain profile. / Proteasome B-type subunit / Proteasome beta-type subunit profile. / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / von Willebrand factor, type A / AAA ATPase, AAA+ lid domain / AAA+ lid domain / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / MPN domain / MPN domain profile. / Nucleophile aminohydrolases, N-terminal / von Willebrand factor A-like domain superfamily / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Armadillo-like helical / Armadillo-type fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Proteasome subunit alpha type / PCI domain-containing protein / AAA domain-containing protein / MPN domain-containing protein / AAA domain-containing protein / VWFA domain-containing protein / AAA domain-containing protein / Proteasome subunit beta / AAA domain-containing protein / PCI domain-containing protein ...Proteasome subunit alpha type / PCI domain-containing protein / AAA domain-containing protein / MPN domain-containing protein / AAA domain-containing protein / VWFA domain-containing protein / AAA domain-containing protein / Proteasome subunit beta / AAA domain-containing protein / PCI domain-containing protein / PCI domain-containing protein / PCI domain-containing protein / Proteasome subunit alpha type / 26S proteasome non-ATPase regulatory subunit 2 homolog / Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit alpha type / 26S proteasome non-ATPase regulatory subunit 1 homolog / PCI domain-containing protein / PCI domain-containing protein / Proteasome subunit beta / AAA domain-containing protein / MPN domain-containing protein / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit beta type-5 / Proteasome subunit alpha type-3 / 26S proteasome regulatory subunit 7
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsKandolf S / Grishkovskaya I
Funding support1 items
OrganizationGrant numberCountry
Other private
CitationJournal: Plant Commun / Year: 2022
Title: Cryo-EM structure of the plant 26S proteasome.
Authors: Susanne Kandolf / Irina Grishkovskaya / Katarina Belačić / Derek L Bolhuis / Sascha Amann / Brent Foster / Richard Imre / Karl Mechtler / Alexander Schleiffer / Hemant D Tagare / Ellen D ...Authors: Susanne Kandolf / Irina Grishkovskaya / Katarina Belačić / Derek L Bolhuis / Sascha Amann / Brent Foster / Richard Imre / Karl Mechtler / Alexander Schleiffer / Hemant D Tagare / Ellen D Zhong / Anton Meinhart / Nicholas G Brown / David Haselbach /
Abstract: Targeted proteolysis is a hallmark of life. It is especially important in long-lived cells that can be found in higher eukaryotes, like plants. This task is mainly fulfilled by the ubiquitin- ...Targeted proteolysis is a hallmark of life. It is especially important in long-lived cells that can be found in higher eukaryotes, like plants. This task is mainly fulfilled by the ubiquitin-proteasome system. Thus, proteolysis by the 26S proteasome is vital to development, immunity, and cell division. Although the yeast and animal proteasomes are well characterized, there is only limited information on the plant proteasome. We determined the first plant 26S proteasome structure from Spinacia oleracea by single-particle electron cryogenic microscopy at an overall resolution of 3.3 Å. We found an almost identical overall architecture of the spinach proteasome compared with the known structures from mammals and yeast. Nevertheless, we noticed a structural difference in the proteolytic active β1 subunit. Furthermore, we uncovered an unseen compression state by characterizing the proteasome's conformational landscape. We suspect that this new conformation of the 20S core protease, in correlation with a partial opening of the unoccupied gate, may contribute to peptide release after proteolysis. Our data provide a structural basis for the plant proteasome, which is crucial for further studies.
History
DepositionJan 21, 2022-
Header (metadata) releaseMay 25, 2022-
Map releaseMay 25, 2022-
SupersessionAug 24, 2022ID: EMD-14177
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14175.png

Downloads & links

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Map

FileDownload / File: emd_14175.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.23 Å/pix.
x 440 pix.
= 541.696 Å		1.23 Å/pix.
x 440 pix.
= 541.696 Å		1.23 Å/pix.
x 440 pix.
= 541.696 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.23113 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0168
Minimum - Maximum-0.023183236 - 1.9318216
Average (Standard dev.)0.0013427478 (±0.025163185)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 541.696 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Spinach 26S proteasome

EntireName: Spinach 26S proteasome
Components
  • Complex: Spinach 26S 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-3
    • 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 beta
    • Protein or peptide: Proteasome subunit beta type-5
    • Protein or peptide: Proteasome subunit beta
    • Protein or peptide: Proteasome subunit beta

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Supramolecule #1: Spinach 26S proteasome

SupramoleculeName: Spinach 26S proteasome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 1.7 MDa

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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: Spinacia oleracea (spinach)
Molecular weightTheoretical: 25.588023 KDa
SequenceString: MGDSQYSFSL TTFSPSGKLV QIEHALTAVG SGQTSLGIKA ANGVVIATEK KLPSILVDEA SVQKIQLLTP NIGVVYSGMG PDSRVLVRK SRKQAEQYYK LYKEPIPVTQ LVRETAAVMQ EFTQSGGVRP FGVSLLIAGF DENGPQLYQV DPSGSYFSWK A SAMGKNVS ...String:
MGDSQYSFSL TTFSPSGKLV QIEHALTAVG SGQTSLGIKA ANGVVIATEK KLPSILVDEA SVQKIQLLTP NIGVVYSGMG PDSRVLVRK SRKQAEQYYK LYKEPIPVTQ LVRETAAVMQ EFTQSGGVRP FGVSLLIAGF DENGPQLYQV DPSGSYFSWK A SAMGKNVS NAKTFLEKRY TDDMELDDAV HTAILTLKEG FEGQISGKNI EIGIIGTDKK FRVLTPAEID DYLGEVE

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: Spinacia oleracea (spinach)
Molecular weightTheoretical: 27.504117 KDa
SequenceString: MSRRYDSRTT IFSPEGRLYQ VEYAMEAIGN AGSAIGILAK DGVVLIGEKK VTSKLLQTST STEKMYKIDD HVACAVAGIM SDANILINT ARVQAQRYTF SYQEPMPVEQ LVQSLCDTKQ GYTQFGGLRP FGVSFLFAGW DKNYGFQLYM SDPSGNYGGW K ATAIGANN ...String:
MSRRYDSRTT IFSPEGRLYQ VEYAMEAIGN AGSAIGILAK DGVVLIGEKK VTSKLLQTST STEKMYKIDD HVACAVAGIM SDANILINT ARVQAQRYTF SYQEPMPVEQ LVQSLCDTKQ GYTQFGGLRP FGVSFLFAGW DKNYGFQLYM SDPSGNYGGW K ATAIGANN QAAQSMLKQD YKDDVTREDA VKLALKVLSK TMDSTSLTSE KLELAEVYLL PSGKVKYQVH SPESLNRLLT ES GLTQPAA ETS

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: Spinacia oleracea (spinach)
Molecular weightTheoretical: 26.844439 KDa
SequenceString: MARYDRAITV FSPDGHLFQV EYALEAVRKG NAAVGVRGTD TVVLGVEKKS AAKLQDSRSV RKIVNLDNHI ALACAGLKAD ARVLINKAR IECQSHKLTL EDPVTVEYIT RYIAGLQQKY TQSGGVRPFG LSTLIVGFDP YTDVPALYQT DPSGTFSAWK A NATGRNSN ...String:
MARYDRAITV FSPDGHLFQV EYALEAVRKG NAAVGVRGTD TVVLGVEKKS AAKLQDSRSV RKIVNLDNHI ALACAGLKAD ARVLINKAR IECQSHKLTL EDPVTVEYIT RYIAGLQQKY TQSGGVRPFG LSTLIVGFDP YTDVPALYQT DPSGTFSAWK A NATGRNSN SIREFLEKNY KETSGQETVK LAIRALLEVV ESGGKNLEVA VMRKEGLHQL EESEIDAIVA EIEAEKAAAE AA KKGPASS

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: Spinacia oleracea (spinach)
Molecular weightTheoretical: 26.027238 KDa
SequenceString: MFLTRTEYDR GVNTFSPEGR LFQVEYAIEA IKLGSTAIGI KTKEGVVLAV EKRITSPLLE PSSVEKIMEI DDHIGCAMSG LIADARTLV EHARVETQNH RFSYGEPMTV ESTTQALCDL ALRFGEGDEE SMSRPFGVSL LIAGHDENGP SLYYTDPSGT F WQCSAKAI ...String:
MFLTRTEYDR GVNTFSPEGR LFQVEYAIEA IKLGSTAIGI KTKEGVVLAV EKRITSPLLE PSSVEKIMEI DDHIGCAMSG LIADARTLV EHARVETQNH RFSYGEPMTV ESTTQALCDL ALRFGEGDEE SMSRPFGVSL LIAGHDENGP SLYYTDPSGT F WQCSAKAI GSGSEGADSS LQEQFRKDLS FQEAETIALS ILKQVMEEKL TPNNVDIAKV SPTYHLYSPS EVEAVIGRL

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: Spinacia oleracea (spinach)
Molecular weightTheoretical: 29.932393 KDa
SequenceString: MFRNQYDTDV TTWSPAGRLF QVEYAMEAVK QGSAAIGLRS KTHVVLACVN KAQSELSSHQ RKIFKVDDHI GVAIAGLTAD GRVLSRYMR SECINYGFTY ESSLPVGRLV VQLADKAQVC TQRSWKRPYG VGLLVGGLDE SGAHLYYNCP SGNYFEYQAF A IGSRSQAA ...String:
MFRNQYDTDV TTWSPAGRLF QVEYAMEAVK QGSAAIGLRS KTHVVLACVN KAQSELSSHQ RKIFKVDDHI GVAIAGLTAD GRVLSRYMR SECINYGFTY ESSLPVGRLV VQLADKAQVC TQRSWKRPYG VGLLVGGLDE SGAHLYYNCP SGNYFEYQAF A IGSRSQAA KTYLERKFDT FDGATRDELI KHALFSIKET LQGEKLTSSV CTISVVGVGE PFQTLDQQMV QDLINSFETV EE EAPAAEE ADAAPEEAAA AVADQGASDE GAAPMEE

UniProtKB: Proteasome subunit alpha type

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Macromolecule #6: Proteasome subunit alpha type-3

MacromoleculeName: Proteasome subunit alpha type-3 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 27.322258 KDa
SequenceString: MSSIGTGYDL SVTTFSPDGR VFQIEYAAKA VDNSGTAVGI KCKDGIVLGV EKLIQSKMML PGSNRRIHSV HRHSGMAVAG LAADGRQIV ARAKSEATNY ESVYGEAVPV KELADRVASY VHLCTLYWWL RPFGCGVILG GYDRDGPQLY MVEPSGISYR Y FGAAIGKG ...String:
MSSIGTGYDL SVTTFSPDGR VFQIEYAAKA VDNSGTAVGI KCKDGIVLGV EKLIQSKMML PGSNRRIHSV HRHSGMAVAG LAADGRQIV ARAKSEATNY ESVYGEAVPV KELADRVASY VHLCTLYWWL RPFGCGVILG GYDRDGPQLY MVEPSGISYR Y FGAAIGKG KQAAKTEIEK LKLSEMTCRE GIIEVAKIIY KVHDEAKDKA FELEMSWICD ESKREHQKVP DNLLQEAKAA AT AALEEMD AD

UniProtKB: Proteasome subunit alpha type-3

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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: Spinacia oleracea (spinach)
Molecular weightTheoretical: 27.211789 KDa
SequenceString: MSRGSGAGYD RHITIFSPEG RLFQVEYAFK AVKSGGVTSI AVRGKDSVCV VTQKKVPDKL LDQTSVSHLF KITKFLGLLA TGMTADARN LVQQARNEAA EFRHKYGYEM PVDALARWIA DKSQVYTQHA YMRPLGVVAI VIGIDEENGP QLFKCDPAGH F YGHKATSA ...String:
MSRGSGAGYD RHITIFSPEG RLFQVEYAFK AVKSGGVTSI AVRGKDSVCV VTQKKVPDKL LDQTSVSHLF KITKFLGLLA TGMTADARN LVQQARNEAA EFRHKYGYEM PVDALARWIA DKSQVYTQHA YMRPLGVVAI VIGIDEENGP QLFKCDPAGH F YGHKATSA GSKDQEAINF LEKKMKNDPA FSYEETVQTA ISALQSVLQE DFKATEIEVG VVQVANPVFR SLTTEEIDEH LT AISERD

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: Spinacia oleracea (spinach)
Molecular weightTheoretical: 25.324434 KDa
SequenceString: MEDLGLNAPH SMGTTIIGVT YKDGVILGAD SRTSTGVYVA NRASDKITQL TDNVYVCRSG SAADSQIVSD YVRYFLHQHT IQLGQPATV KVAANLVRLL AYGNKDTLQT GMIVGGWDKY EGGKIYGIPL GGTIIEQPFS IGGSGSSYLY GFLDQAWKDG M SKDEAEEL ...String:
MEDLGLNAPH SMGTTIIGVT YKDGVILGAD SRTSTGVYVA NRASDKITQL TDNVYVCRSG SAADSQIVSD YVRYFLHQHT IQLGQPATV KVAANLVRLL AYGNKDTLQT GMIVGGWDKY EGGKIYGIPL GGTIIEQPFS IGGSGSSYLY GFLDQAWKDG M SKDEAEEL VKKAVSLAIA RDGASGGVVR TVIINEEGVT RNFYPGDQLP LWHEELEPQN SLLDIWGAAA ASPVPMTE

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: Spinacia oleracea (spinach)
Molecular weightTheoretical: 29.404385 KDa
SequenceString: MTNGAFEVPA KGGFSFDNCK RNEMLLNKGL KAPGFLKTGT TIVGLVYQDG VILGADTRAT EGPIVADKNC EKIHYMAPNI YCCGAGTAA DTEAVTDMVS SQLKLHRYHT GRESRVITAL TLLKSHLFRY QGHVSAALVL GGVDVSGPHL HTIYPHGSTD T LPFATMGS ...String:
MTNGAFEVPA KGGFSFDNCK RNEMLLNKGL KAPGFLKTGT TIVGLVYQDG VILGADTRAT EGPIVADKNC EKIHYMAPNI YCCGAGTAA DTEAVTDMVS SQLKLHRYHT GRESRVITAL TLLKSHLFRY QGHVSAALVL GGVDVSGPHL HTIYPHGSTD T LPFATMGS GSLAAMSVFE SKYREGLTRD EGVKIVCEAI ASGIFNDLGS GSNVDVCVIT KGNVEYLRNH VQPNPRTYTS AK GYTFSKP TEVLSTKVTA LAQRAVVTER GDAMEEE

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: Spinacia oleracea (spinach)
Molecular weightTheoretical: 22.847109 KDa
SequenceString: MSIFEYNGSA TVAMVGKNCI AIGSDRRLGV QLQTIATDFQ RIFQIHDRLF IGLSGLGSDA QTLYQRLVFR HKLYQLREER DMKPETFAN LVSAILYEKR FGPYFCQPVI AGLGDDNKPF ICTMDSIGAK ELAKDFVVAG TASESLYGAC ESMYKPDMEP E ELFETVSQ ...String:
MSIFEYNGSA TVAMVGKNCI AIGSDRRLGV QLQTIATDFQ RIFQIHDRLF IGLSGLGSDA QTLYQRLVFR HKLYQLREER DMKPETFAN LVSAILYEKR FGPYFCQPVI AGLGDDNKPF ICTMDSIGAK ELAKDFVVAG TASESLYGAC ESMYKPDMEP E ELFETVSQ ALQASVDRDC LSGWGGHVYI VTPTEIKEHI LKGRMD

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: Spinacia oleracea (spinach)
Molecular weightTheoretical: 22.950082 KDa
SequenceString: MECVFGLVGN GFAIIAADTS AVNSILVHKT NEDKIMKLDS HKLMGASGEA GDRVQFTEFV QKNVSLYQFR NGIPLTTAAA ANFTRGELA TALRKNPYSV NIILAGFDQD TGPSLYFIDY IATLHKVDKA AFGYGSYFAL AMMDRHYRSD MSVDEAIKLV D ECIAEIRT ...String:
MECVFGLVGN GFAIIAADTS AVNSILVHKT NEDKIMKLDS HKLMGASGEA GDRVQFTEFV QKNVSLYQFR NGIPLTTAAA ANFTRGELA TALRKNPYSV NIILAGFDQD TGPSLYFIDY IATLHKVDKA AFGYGSYFAL AMMDRHYRSD MSVDEAIKLV D ECIAEIRT RLVVAPPNFV IKIVDKDGAR EFAWRQSIKD QGVEDANAAS A

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 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 29.652654 KDa
SequenceString: MKLDTSGLES TAPIFRRSDF VFDGLQMTPS FDLPNPTDFD GFQKEAVQMV KPAKGTTTLA FIFKHGVMVA ADSRASMGGY ISSQSVKKI IEINPYMLGT MAGGAADCQF WHRNLGIKCR LHELANKRRI SVTGASKLLA NILYNYRGMG LSVGTMIAGW D ETGPGLYY ...String:
MKLDTSGLES TAPIFRRSDF VFDGLQMTPS FDLPNPTDFD GFQKEAVQMV KPAKGTTTLA FIFKHGVMVA ADSRASMGGY ISSQSVKKI IEINPYMLGT MAGGAADCQF WHRNLGIKCR LHELANKRRI SVTGASKLLA NILYNYRGMG LSVGTMIAGW D ETGPGLYY VDSEGGRLKG MRFSVGSGSP YAYGVLDNGY KYDMTVEEAS ELARRAIYHA TYRDGASGGV VSVYHVGPDG WK KVTGDDV GDLHFQYYPV VPATVEQEMV EVVGA

UniProtKB: Proteasome subunit beta type-5

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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: Spinacia oleracea (spinach)
Molecular weightTheoretical: 24.835199 KDa
SequenceString: MTKEHANWSP YDFNGGTCVA VAGADYCVIA ADTRMSTGYN ILTRDYSKIC KLAEKSVLAS SGFQADVRAL QKHLDARHLI YQHQHNKQM SCPAMAQLLS NTLYYKRFFP YYAFNVLGGL DNEGKGCVFT YDAVGSYEKV GYSSQGSGAK LIMPFLDNQL K SPSPLLIP ...String:
MTKEHANWSP YDFNGGTCVA VAGADYCVIA ADTRMSTGYN ILTRDYSKIC KLAEKSVLAS SGFQADVRAL QKHLDARHLI YQHQHNKQM SCPAMAQLLS NTLYYKRFFP YYAFNVLGGL DNEGKGCVFT YDAVGSYEKV GYSSQGSGAK LIMPFLDNQL K SPSPLLIP AQDAVTPLSE SEAIDLVRTA FASATERDIY TGDKLEILVL NKEGLRREYM ELRLD

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: Spinacia oleracea (spinach)
Molecular weightTheoretical: 27.09877 KDa
SequenceString: MDPKNTSPLL VDDIQRTQYP YVTGTSVIGI KYKDGILIAA DMGGSYGSTL RYKSVERLKG IGKHSLLGAS GEISDFQELL RYLDDLILY DNMWDDGNSF GPKEVHNYLT RVMYNRRNKF NPLWNSLVLG GVKNGQKYLG TVNMIGVHYQ DNHVATGFGN H LAVPILRD ...String:
MDPKNTSPLL VDDIQRTQYP YVTGTSVIGI KYKDGILIAA DMGGSYGSTL RYKSVERLKG IGKHSLLGAS GEISDFQELL RYLDDLILY DNMWDDGNSF GPKEVHNYLT RVMYNRRNKF NPLWNSLVLG GVKNGQKYLG TVNMIGVHYQ DNHVATGFGN H LAVPILRD EWKEDLSFED GVRLLEKCMR VLLYRDRSAV NKLQIAKITE EGGVTISPPY SLKTYWEFAA FKNPTAGAEG SW

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

Concentration0.02 mg/mL
BufferpH: 6.5
Component:
ConcentrationFormulaName
25.0 mMBis-Trisbis(2-hydroxyethyl)amino-tris(hydroxymethyl)methan
50.0 mMKClpotassium chloride
5.0 mMMgCl2magnedium chloride
5.0 %glycerolglycerol
20.0 mMATPadenosine triphosphate
5.0 mMDTTdithiothreitol
5.0 %PVPpolyvinylpolypyrrolidone
2.0 mMPMSFphenylmethylsulfonyl fluoride
GridModel: Quantifoil R3.5/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: FEI FALCON III (4k x 4k) / #0 - Detector mode: INTEGRATING / #0 - Number real images: 24769 / #0 - Average electron dose: 80.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: FEI FALCON III (4k x 4k) / #1 - Detector mode: INTEGRATING / #1 - Digitization - Dimensions - Width: 4096 pixel / #1 - Digitization - Dimensions - Height: 4096 pixel / #1 - Number real images: 8089 / #1 - Average electron dose: 50.0 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: 4.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
Particle selectionNumber selected: 951422
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.0) / Number images used: 951422
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 3.0)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 3.0)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.0)

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Atomic model buiding 1

Initial modelPDB ID:

6msb


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 109.9
Output model

PDB-7qve:
Spinach 20S proteasome

PDB-8amz:
Spinach 19S proteasome

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