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- EMDB-47725: Nub1/Fat10-processing human 26S proteasome bound to Txnl1 with Rp... -

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Basic information

Entry
Database: EMDB / ID: EMD-47725
TitleNub1/Fat10-processing human 26S proteasome bound to Txnl1 with Rpt3 at top of spiral staircase (locally refined on the AAA+ motor)
Map data
Sample
  • Complex: Human 26S proteasome complexed with Nub1 and Fat 10 RPT3 at the top
    • Protein or peptide: x 15 types
  • Ligand: x 4 types
Keywords26S Proteasome / MOTOR PROTEIN / HYDROLASE-PROTEIN BINDING complex
Function / homology
Function and homology information


positive regulation of inclusion body assembly / thyrotropin-releasing hormone receptor binding / nuclear proteasome complex / host-mediated perturbation of viral transcription / proteasome accessory complex / purine ribonucleoside triphosphate binding / CD8-positive, alpha-beta T cell differentiation / thymic T cell selection / cytosolic proteasome complex / CD8-positive, alpha-beta T cell homeostasis ...positive regulation of inclusion body assembly / thyrotropin-releasing hormone receptor binding / nuclear proteasome complex / host-mediated perturbation of viral transcription / proteasome accessory complex / purine ribonucleoside triphosphate binding / CD8-positive, alpha-beta T cell differentiation / thymic T cell selection / cytosolic proteasome complex / CD8-positive, alpha-beta T cell homeostasis / positive regulation of proteasomal protein catabolic process / proteasome-activating activity / Antigen processing: Ub, ATP-independent proteasomal degradation / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / negative regulation of programmed cell death / negative regulation of regulatory T cell differentiation / T-helper 1 cell differentiation / protein K63-linked deubiquitination / cellular response to type I interferon / metal-dependent deubiquitinase activity / Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Proteasome assembly / T-helper 17 cell differentiation / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / Cross-presentation of soluble exogenous antigens (endosomes) / transcription factor binding / Somitogenesis / flagellated sperm motility / K63-linked deubiquitinase activity / proteasome binding / myofibril / positive regulation of RNA polymerase II transcription preinitiation complex assembly / proteasomal ubiquitin-independent protein catabolic process / general transcription initiation factor binding / proteasome storage granule / AMPK-induced ERAD and lysosome mediated degradation of PD-L1(CD274) / protein deubiquitination / NF-kappaB binding / endopeptidase activator activity / proteasome core complex, alpha-subunit complex / GSK3B-mediated proteasomal degradation of PD-L1(CD274) / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / SPOP-mediated proteasomal degradation of PD-L1(CD274) / immune system process / regulation of G1/S transition of mitotic cell cycle / regulation of macroautophagy / positive regulation of interleukin-2 production / ERAD pathway / ciliary tip / Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / response to type II interferon / inclusion body / TBP-class protein binding / proteasome complex / : / regulation of proteasomal protein catabolic process / sarcomere / sperm end piece / Regulation of activated PAK-2p34 by proteasome mediated degradation / proteasomal protein catabolic process / Autodegradation of Cdh1 by Cdh1:APC/C / negative regulation of inflammatory response to antigenic stimulus / APC/C:Cdc20 mediated degradation of Securin / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins / lipopolysaccharide binding / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / P-body / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of DVL / Degradation of AXIN / Degradation of CRY and PER proteins / meiotic cell cycle / Hh mutants are degraded by ERAD / Activation of NF-kappaB in B cells / G2/M Checkpoints / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / Autodegradation of the E3 ubiquitin ligase COP1 / Regulation of RUNX3 expression and activity / Defective CFTR causes cystic fibrosis / double-strand break repair via homologous recombination / response to virus / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / Hedgehog 'on' state / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Vif-mediated degradation of APOBEC3G / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome
Similarity search - Function
: / 26S proteasome regulatory subunit RPN11 C-terminal domain / : / 26S proteasome regulatory subunit 7, OB domain / : / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / Proteasome subunit alpha 1 / : / JAB1/Mov34/MPN/PAD-1 ubiquitin protease ...: / 26S proteasome regulatory subunit RPN11 C-terminal domain / : / 26S proteasome regulatory subunit 7, OB domain / : / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / Proteasome subunit alpha 1 / : / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Proteasome subunit alpha5 / Proteasome subunit alpha6 / 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 subunit / Proteasome, subunit alpha/beta / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / AAA ATPase, AAA+ lid domain / AAA+ lid domain / MPN domain / MPN domain profile. / ATPase, AAA-type, conserved site / AAA-protein family signature. / Nucleophile aminohydrolases, N-terminal / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / 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
Ubiquitin C-terminal hydrolase PSMD14 / Proteasome subunit alpha type-7 / 26S proteasome regulatory subunit 6A / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-4 / Proteasome subunit alpha type-5 / 26S proteasome regulatory subunit 7 / 26S proteasome regulatory subunit 6B ...Ubiquitin C-terminal hydrolase PSMD14 / Proteasome subunit alpha type-7 / 26S proteasome regulatory subunit 6A / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-4 / Proteasome subunit alpha type-5 / 26S proteasome regulatory subunit 7 / 26S proteasome regulatory subunit 6B / Proteasome subunit alpha type-6 / 26S proteasome regulatory subunit 4 / 26S proteasome regulatory subunit 8 / 26S proteasome regulatory subunit 10B
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.62 Å
AuthorsArkinson C / Gee CL / Martin A
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: bioRxiv / Year: 2024
Title: Structural landscape of AAA+ ATPase motor states in the substrate-degrading human 26S proteasome reveals conformation-specific binding of TXNL1.
Authors: Connor Arkinson / Christine L Gee / Zeyuan Zhang / Ken C Dong / Andreas Martin /
Abstract: The 26S proteasome targets many cellular proteins for degradation during general homeostasis, protein quality control, and the regulation of vital processes. A broad range of proteasome-interacting ...The 26S proteasome targets many cellular proteins for degradation during general homeostasis, protein quality control, and the regulation of vital processes. A broad range of proteasome-interacting cofactors thereby modulates these functions and aids in substrate degradation. Here, we solved several high-resolution structures of the redox active cofactor TXNL1 bound to the human 26S proteasome at saturating and sub-stoichiometric concentrations by time resolved cryo-EM. We identified distinct binding modes of TXNL1 that depend on the proteasome conformational and ATPase motor states. Together with biophysical and biochemical experiments, our structural studies reveal that the resting-state proteasome prior to substrate engagement with the ATPase motor binds TXNL1 with low affinity and in variable positions on top of the Rpn11 deubiquitinase. In contrast, the actively degrading proteasome shows additional interactions leading to high-affinity TXNL1 binding, whereby TXNL1's C-terminal tail covers the catalytic groove of the Rpn11 deubiquitinase and coordinates the active-site Zn. Furthermore, these cryo-EM structures of the degrading proteasome capture the ATPase hexamer in all registers of spiral-staircase arrangements and thus visualize the complete ATP-hydrolysis cycle of the AAA+ motor, indicating temporally asymmetric hydrolysis and conformational changes in bursts during mechanical substrate unfolding and translocation. Remarkably, we catch the proteasome in the act of unfolding the beta-barrel mEos3.2 substrate while the ATPase hexamer is in a particular spiral staircase register. Our findings challenge current models for protein translocation through hexameric AAA+ motors and reveal how the proteasome uses its distinct but broad range of conformational states to coordinate cofactor binding and substrate processing.
History
DepositionNov 5, 2024-
Header (metadata) releaseDec 4, 2024-
Map releaseDec 4, 2024-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47725.png

Downloads & links

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Map

FileDownload / File: emd_47725.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 340 pix.
= 356.32 Å		1.05 Å/pix.
x 340 pix.
= 356.32 Å		1.05 Å/pix.
x 340 pix.
= 356.32 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.048 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.59750855 - 0.8541773
Average (Standard dev.)0.0015103008 (±0.03627156)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 356.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_47725_additional_1.map
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Half map: #2

Fileemd_47725_half_map_1.map
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Half map: #1

Fileemd_47725_half_map_2.map
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Sample components

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Entire : Human 26S proteasome complexed with Nub1 and Fat 10 RPT3 at the top

EntireName: Human 26S proteasome complexed with Nub1 and Fat 10 RPT3 at the top
Components
  • Complex: Human 26S proteasome complexed with Nub1 and Fat 10 RPT3 at the top
    • Protein or peptide: 26S proteasome regulatory subunit 7
    • Protein or peptide: 26S protease regulatory subunit 8
    • Protein or peptide: 26S protease regulatory subunit 10B
    • Protein or peptide: Proteasome subunit alpha type-6
    • Protein or peptide: Proteasome subunit alpha type-2
    • Protein or peptide: Proteasome subunit alpha type-4
    • Protein or peptide: Proteasome subunit alpha type-7
    • Protein or peptide: Proteasome subunit alpha type-1
    • Protein or peptide: Proteasome subunit alpha type-3
    • Protein or peptide: substrate
    • Protein or peptide: 26S proteasome regulatory subunit 6B
    • Protein or peptide: 26S proteasome regulatory subunit 4
    • Protein or peptide: 26S proteasome regulatory subunit 6A
    • Protein or peptide: Proteasome subunit alpha type-5
    • Protein or peptide: 26S proteasome non-ATPase regulatory subunit 14
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: Human 26S proteasome complexed with Nub1 and Fat 10 RPT3 at the top

SupramoleculeName: Human 26S proteasome complexed with Nub1 and Fat 10 RPT3 at the top
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#15
Source (natural)Organism: Homo sapiens (human) / Strain: HEK293
Molecular weightTheoretical: 2.6 MDa

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Macromolecule #1: 26S proteasome regulatory subunit 7

MacromoleculeName: 26S proteasome regulatory subunit 7 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.642703 KDa
SequenceString: MPDYLGADQR KTKEDEKDDK PIRALDEGDI ALLKTYGQST YSRQIKQVED DIQQLLKKIN ELTGIKESDT GLAPPALWDL AADKQTLQS EQPLQVARCT KIINADSEDP KYIINVKQFA KFVVDLSDQV APTDIEEGMR VGVDRNKYQI HIPLPPIADP T VTMMQVEE ...String:
MPDYLGADQR KTKEDEKDDK PIRALDEGDI ALLKTYGQST YSRQIKQVED DIQQLLKKIN ELTGIKESDT GLAPPALWDL AADKQTLQS EQPLQVARCT KIINADSEDP KYIINVKQFA KFVVDLSDQV APTDIEEGMR VGVDRNKYQI HIPLPPIADP T VTMMQVEE KPDVTYSDVG GCKEQIEKLR EVVETPLLHP ERFVNLGIEP PKGVLLFGPP GTGKTLCARA VANRTDACFI RV IGSELVQ KYVGEGARMV RELFEMARTK KACLIFFDEI DAIGGARFDD GAGGDNEVQR TMLELINQLD GFDPRGNIKV LMA TNRPDT LDPALMRPGR LDRKIEFSLP DLEGRTHIFK IHARSMSVER DIRFELLARL CPNSTGAEIR SVCTEAGMFA IRAR RKIAT EKDFLEAVNK VIKSYAKFSA TPRYMTYN

UniProtKB: 26S proteasome regulatory subunit 7

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Macromolecule #2: 26S protease regulatory subunit 8

MacromoleculeName: 26S protease regulatory subunit 8 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.694047 KDa
SequenceString: MALDGPEQME LEEGKAGSGL RQYYLSKIEE LQLIVNDKSQ NLRRLQAQRN ELNAKVRLLR EELQLLQEQG SYVGEVVRAM DKKKVLVKV HPEGKFVVDV DKNIDINDVT PNCRVALRND SYTLHKILPN KVDPLVSLMM VEKVPDSTYE MIGGLDKQIK E IKEVIELP ...String:
MALDGPEQME LEEGKAGSGL RQYYLSKIEE LQLIVNDKSQ NLRRLQAQRN ELNAKVRLLR EELQLLQEQG SYVGEVVRAM DKKKVLVKV HPEGKFVVDV DKNIDINDVT PNCRVALRND SYTLHKILPN KVDPLVSLMM VEKVPDSTYE MIGGLDKQIK E IKEVIELP VKHPELFEAL GIAQPKGVLL YGPPGTGKTL LARAVAHHTD CTFIRVSGSE LVQKFIGEGA RMVRELFVMA RE HAPSIIF MDEIDSIGSS RLEGGSGGDS EVQRTMLELL NQLDGFEATK NIKVIMATNR IDILDSALLR PGRIDRKIEF PPP NEEARL DILKIHSRKM NLTRGINLRK IAELMPGASG AEVKGVCTEA GMYALRERRV HVTQEDFEMA VAKVMQKDSE KNMS IKKLW K

UniProtKB: 26S proteasome regulatory subunit 8

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Macromolecule #3: 26S protease regulatory subunit 10B

MacromoleculeName: 26S protease regulatory subunit 10B / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.241008 KDa
SequenceString: MADPRDKALQ DYRKKLLEHK EIDGRLKELR EQLKELTKQY EKSENDLKAL QSVGQIVGEV LKQLTEEKFI VKATNGPRYV VGCRRQLDK SKLKPGTRVA LDMTTLTIMR YLPREVDPLV YNMSHEDPGN VSYSEIGGLS EQIRELREVI ELPLTNPELF Q RVGIIPPK ...String:
MADPRDKALQ DYRKKLLEHK EIDGRLKELR EQLKELTKQY EKSENDLKAL QSVGQIVGEV LKQLTEEKFI VKATNGPRYV VGCRRQLDK SKLKPGTRVA LDMTTLTIMR YLPREVDPLV YNMSHEDPGN VSYSEIGGLS EQIRELREVI ELPLTNPELF Q RVGIIPPK GCLLYGPPGT GKTLLARAVA SQLDCNFLKV VSSSIVDKYI GESARLIREM FNYARDHQPC IIFMDEIDAI GG RRFSEGT SADREIQRTL MELLNQMDGF DTLHRVKMIM ATNRPDTLDP ALLRPGRLDR KIHIDLPNEQ ARLDILKIHA GPI TKHGEI DYEAIVKLSD GFNGADLRNV CTEAGMFAIR ADHDFVVQED FMKAVRKVAD SKKLESKLDY KPV

UniProtKB: 26S proteasome regulatory subunit 10B

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Macromolecule #4: Proteasome subunit alpha type-6

MacromoleculeName: Proteasome subunit alpha type-6 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.432459 KDa
SequenceString: MSRGSSAGFD RHITIFSPEG RLYQVEYAFK AINQGGLTSV AVRGKDCAVI VTQKKVPDKL LDSSTVTHLF KITENIGCVM TGMTADSRS QVQRARYEAA NWKYKYGYEI PVDMLCKRIA DISQVYTQNA EMRPLGCCMI LIGIDEEQGP QVYKCDPAGY Y CGFKATAA ...String:
MSRGSSAGFD RHITIFSPEG RLYQVEYAFK AINQGGLTSV AVRGKDCAVI VTQKKVPDKL LDSSTVTHLF KITENIGCVM TGMTADSRS QVQRARYEAA NWKYKYGYEI PVDMLCKRIA DISQVYTQNA EMRPLGCCMI LIGIDEEQGP QVYKCDPAGY Y CGFKATAA GVKQTESTSF LEKKVKKKFD WTFEQTVETA ITCLSTVLSI DFKPSEIEVG VVTVENPKFR ILTEAEIDAH LV ALAERD

UniProtKB: Proteasome subunit alpha type-6

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Macromolecule #5: Proteasome subunit alpha type-2

MacromoleculeName: Proteasome subunit alpha type-2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.924406 KDa
SequenceString: MAERGYSFSL TTFSPSGKLV QIEYALAAVA GGAPSVGIKA ANGVVLATEK KQKSILYDER SVHKVEPITK HIGLVYSGMG PDYRVLVHR ARKLAQQYYL VYQEPIPTAQ LVQRVASVMQ EYTQSGGVRP FGVSLLICGW NEGRPYLFQS DPSGAYFAWK A TAHGKNYV ...String:
MAERGYSFSL TTFSPSGKLV QIEYALAAVA GGAPSVGIKA ANGVVLATEK KQKSILYDER SVHKVEPITK HIGLVYSGMG PDYRVLVHR ARKLAQQYYL VYQEPIPTAQ LVQRVASVMQ EYTQSGGVRP FGVSLLICGW NEGRPYLFQS DPSGAYFAWK A TAHGKNYV NGKTFLEHHY NEDLELEDAI HTAILTLKES FEGQMTEDNI EVGICNEAGF RRLTPTEVKD YLAAIA

UniProtKB: Proteasome subunit alpha type-2

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Macromolecule #6: Proteasome subunit alpha type-4

MacromoleculeName: Proteasome subunit alpha type-4 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.525842 KDa
SequenceString: MSRRYDSRTT IFSPEGRLYQ VEYAMEAIGH AGTCLGILAN DGVLLAAERR NIHKLLDEVF FSEKIYKLNE DMACSVAGIT SDANVLTNE LRLIAQRYLL QYQEPIPCEQ LVTALCDIKQ AYTQFGGKRP FGVSLLYIGW DKHYGFQLYQ SDPSGNYGGW K ATCIGNNS ...String:
MSRRYDSRTT IFSPEGRLYQ VEYAMEAIGH AGTCLGILAN DGVLLAAERR NIHKLLDEVF FSEKIYKLNE DMACSVAGIT SDANVLTNE LRLIAQRYLL QYQEPIPCEQ LVTALCDIKQ AYTQFGGKRP FGVSLLYIGW DKHYGFQLYQ SDPSGNYGGW K ATCIGNNS AAAVSMLKQD YKEGEMTLKS ALALAIKVLN KTMDVSKLSA EKVEIATLTR ENGKTVIRVL KQKEVEQLIK KH EEEEAKA EREKKEKEQK EKDK

UniProtKB: Proteasome subunit alpha type-4

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Macromolecule #7: Proteasome subunit alpha type-7

MacromoleculeName: Proteasome subunit alpha type-7 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.929891 KDa
SequenceString: MSYDRAITVF SPDGHLFQVE YAQEAVKKGS TAVGVRGRDI VVLGVEKKSV AKLQDERTVR KICALDDNVC MAFAGLTADA RIVINRARV ECQSHRLTVE DPVTVEYITR YIASLKQRYT QSNGRRPFGI SALIVGFDFD GTPRLYQTDP SGTYHAWKAN A IGRGAKSV ...String:
MSYDRAITVF SPDGHLFQVE YAQEAVKKGS TAVGVRGRDI VVLGVEKKSV AKLQDERTVR KICALDDNVC MAFAGLTADA RIVINRARV ECQSHRLTVE DPVTVEYITR YIASLKQRYT QSNGRRPFGI SALIVGFDFD GTPRLYQTDP SGTYHAWKAN A IGRGAKSV REFLEKNYTD EAIETDDLTI KLVIKALLEV VQSGGKNIEL AVMRRDQSLK ILNPEEIEKY VAEIEKEKEE NE KKKQKKA S

UniProtKB: Proteasome subunit alpha type-7

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Macromolecule #8: Proteasome subunit alpha type-1

MacromoleculeName: Proteasome subunit alpha type-1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.595627 KDa
SequenceString: MFRNQYDNDV TVWSPQGRIH QIEYAMEAVK QGSATVGLKS KTHAVLVALK RAQSELAAHQ KKILHVDNHI GISIAGLTAD ARLLCNFMR QECLDSRFVF DRPLPVSRLV SLIGSKTQIP TQRYGRRPYG VGLLIAGYDD MGPHIFQTCP SANYFDCRAM S IGARSQSA ...String:
MFRNQYDNDV TVWSPQGRIH QIEYAMEAVK QGSATVGLKS KTHAVLVALK RAQSELAAHQ KKILHVDNHI GISIAGLTAD ARLLCNFMR QECLDSRFVF DRPLPVSRLV SLIGSKTQIP TQRYGRRPYG VGLLIAGYDD MGPHIFQTCP SANYFDCRAM S IGARSQSA RTYLERHMSE FMECNLNELV KHGLRALRET LPAEQDLTTK NVSIGIVGKD LEFTIYDDDD VSPFLEGLEE RP QRKAQPA QPADEPAEKA DEPMEH

UniProtKB: Proteasome subunit alpha type-1

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Macromolecule #9: Proteasome subunit alpha type-3

MacromoleculeName: Proteasome subunit alpha type-3 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.469252 KDa
SequenceString: MSSIGTGYDL SASTFSPDGR VFQVEYAMKA VENSSTAIGI RCKDGVVFGV EKLVLSKLYE EGSNKRLFNV DRHVGMAVAG LLADARSLA DIAREEASNF RSNFGYNIPL KHLADRVAMY VHAYTLYSAV RPFGCSFMLG SYSVNDGAQL YMIDPSGVSY G YWGCAIGK ...String:
MSSIGTGYDL SASTFSPDGR VFQVEYAMKA VENSSTAIGI RCKDGVVFGV EKLVLSKLYE EGSNKRLFNV DRHVGMAVAG LLADARSLA DIAREEASNF RSNFGYNIPL KHLADRVAMY VHAYTLYSAV RPFGCSFMLG SYSVNDGAQL YMIDPSGVSY G YWGCAIGK ARQAAKTEIE KLQMKEMTCR DIVKEVAKII YIVHDEVKDK AFELELSWVG ELTNGRHEIV PKDIREEAEK YA KESLKEE DESDDDNM

UniProtKB: Proteasome subunit alpha type-3

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Macromolecule #10: substrate

MacromoleculeName: substrate / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.209482 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)

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Macromolecule #11: 26S proteasome regulatory subunit 6B

MacromoleculeName: 26S proteasome regulatory subunit 6B / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.426141 KDa
SequenceString: MEEIGILVEK AQDEIPALSV SRPQTGLSFL GPEPEDLEDL YSRYKKLQQE LEFLEVQEEY IKDEQKNLKK EFLHAQEEVK RIQSIPLVI GQFLEAVDQN TAIVGSTTGS NYYVRILSTI DRELLKPNAS VALHKHSNAL VDVLPPEADS SIMMLTSDQK P DVMYADIG ...String:
MEEIGILVEK AQDEIPALSV SRPQTGLSFL GPEPEDLEDL YSRYKKLQQE LEFLEVQEEY IKDEQKNLKK EFLHAQEEVK RIQSIPLVI GQFLEAVDQN TAIVGSTTGS NYYVRILSTI DRELLKPNAS VALHKHSNAL VDVLPPEADS SIMMLTSDQK P DVMYADIG GMDIQKQEVR EAVELPLTHF ELYKQIGIDP PRGVLMYGPP GCGKTMLAKA VAHHTTAAFI RVVGSEFVQK YL GEGPRMV RDVFRLAKEN APAIIFIDEI DAIATKRFDA QTGADREVQR ILLELLNQMD GFDQNVNVKV IMATNRADTL DPA LLRPGR LDRKIEFPLP DRRQKRLIFS TITSKMNLSE EVDLEDYVAR PDKISGADIN SICQESGMLA VRENRYIVLA KDFE KAYKT VIKKDEQEHE FYK

UniProtKB: 26S proteasome regulatory subunit 6B

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Macromolecule #12: 26S proteasome regulatory subunit 4

MacromoleculeName: 26S proteasome regulatory subunit 4 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.260504 KDa
SequenceString: MGQSQSGGHG PGGGKKDDKD KKKKYEPPVP TRVGKKKKKT KGPDAASKLP LVTPHTQCRL KLLKLERIKD YLLMEEEFIR NQEQMKPLE EKQEEERSKV DDLRGTPMSV GTLEEIIDDN HAIVSTSVGS EHYVSILSFV DKDLLEPGCS VLLNHKVHAV I GVLMDDTD ...String:
MGQSQSGGHG PGGGKKDDKD KKKKYEPPVP TRVGKKKKKT KGPDAASKLP LVTPHTQCRL KLLKLERIKD YLLMEEEFIR NQEQMKPLE EKQEEERSKV DDLRGTPMSV GTLEEIIDDN HAIVSTSVGS EHYVSILSFV DKDLLEPGCS VLLNHKVHAV I GVLMDDTD PLVTVMKVEK APQETYADIG GLDNQIQEIK ESVELPLTHP EYYEEMGIKP PKGVILYGPP GTGKTLLAKA VA NQTSATF LRVVGSELIQ KYLGDGPKLV RELFRVAEEH APSIVFIDEI DAIGTKRYDS NSGGEREIQR TMLELLNQLD GFD SRGDVK VIMATNRIET LDPALIRPGR IDRKIEFPLP DEKTKKRIFQ IHTSRMTLAD DVTLDDLIMA KDDLSGADIK AICT EAGLM ALRERRMKVT NEDFKKSKEN VLYKKQEGTP EGLYL

UniProtKB: 26S proteasome regulatory subunit 4

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Macromolecule #13: 26S proteasome regulatory subunit 6A

MacromoleculeName: 26S proteasome regulatory subunit 6A / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.266457 KDa
SequenceString: MNLLPNIESP VTRQEKMATV WDEAEQDGIG EEVLKMSTEE IIQRTRLLDS EIKIMKSEVL RVTHELQAMK DKIKENSEKI KVNKTLPYL VSNVIELLDV DPNDQEEDGA NIDLDSQRKG KCAVIKTSTR QTYFLPVIGL VDAEKLKPGD LVGVNKDSYL I LETLPTEY ...String:
MNLLPNIESP VTRQEKMATV WDEAEQDGIG EEVLKMSTEE IIQRTRLLDS EIKIMKSEVL RVTHELQAMK DKIKENSEKI KVNKTLPYL VSNVIELLDV DPNDQEEDGA NIDLDSQRKG KCAVIKTSTR QTYFLPVIGL VDAEKLKPGD LVGVNKDSYL I LETLPTEY DSRVKAMEVD ERPTEQYSDI GGLDKQIQEL VEAIVLPMNH KEKFENLGIQ PPKGVLMYGP PGTGKTLLAR AC AAQTKAT FLKLAGPQLV QMFIGDGAKL VRDAFALAKE KAPSIIFIDE LDAIGTKRFD SEKAGDREVQ RTMLELLNQL DGF QPNTQV KVIAATNRVD ILDPALLRSG RLDRKIEFPM PNEEARARIM QIHSRKMNVS PDVNYEELAR CTDDFNGAQC KAVC VEAGM IALRRGATEL THEDYMEGIL EVQAKKKANL QYYA

UniProtKB: 26S proteasome regulatory subunit 6A

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Macromolecule #14: Proteasome subunit alpha type-5

MacromoleculeName: Proteasome subunit alpha type-5 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.435977 KDa
SequenceString: MFLTRSEYDR GVNTFSPEGR LFQVEYAIEA IKLGSTAIGI QTSEGVCLAV EKRITSPLME PSSIEKIVEI DAHIGCAMSG LIADAKTLI DKARVETQNH WFTYNETMTV ESVTQAVSNL ALQFGEEDAD PGAMSRPFGV ALLFGGVDEK GPQLFHMDPS G TFVQCDAR ...String:
MFLTRSEYDR GVNTFSPEGR LFQVEYAIEA IKLGSTAIGI QTSEGVCLAV EKRITSPLME PSSIEKIVEI DAHIGCAMSG LIADAKTLI DKARVETQNH WFTYNETMTV ESVTQAVSNL ALQFGEEDAD PGAMSRPFGV ALLFGGVDEK GPQLFHMDPS G TFVQCDAR AIGSASEGAQ SSLQEVYHKS MTLKEAIKSS LIILKQVMEE KLNATNIELA TVQPGQNFHM FTKEELEEVI KD I

UniProtKB: Proteasome subunit alpha type-5

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Macromolecule #15: 26S proteasome non-ATPase regulatory subunit 14

MacromoleculeName: 26S proteasome non-ATPase regulatory subunit 14 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.940898 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDRLLRLGGG MPGLGQGPPT DAPAVDTAEQ VYISSLALLK MLKHGRAGVP MEVMGLMLGE FVDDYTVRVI DVFAMPQSGT GVSVEAVDP VFQAKMLDML KQTGRPEMVV GWYHSHPGFG CWLSGVDINT QQSFEALSER AVAVVVDPIQ SVKGKVVIDA F RLINANMM ...String:
MDRLLRLGGG MPGLGQGPPT DAPAVDTAEQ VYISSLALLK MLKHGRAGVP MEVMGLMLGE FVDDYTVRVI DVFAMPQSGT GVSVEAVDP VFQAKMLDML KQTGRPEMVV GWYHSHPGFG CWLSGVDINT QQSFEALSER AVAVVVDPIQ SVKGKVVIDA F RLINANMM VLGHEPRQTT SNLGHLNKPS IQALIHGLNR HYYSITINYR KNELEQKMLL NLHKKSWMEG LTLQDYSEHC KH NESVVKE MLELAKNYNK AVEEEDKMTP EQLAIKNVGK QDPKRHLEEH VDVLMTSNIV QCLAAMLDTV VFKLINHHHH HHD YDIPTT ASENLYFQGE LGMRGSAGKA GEGEIPAPLA GTVSKILVKE GDTVKAGQTV LVLEAMKMET EINAPTDGKV EKVL VKERD AVQGGQGLIK IGVHHHHHH

UniProtKB: Ubiquitin C-terminal hydrolase PSMD14

+
Macromolecule #16: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 16 / Number of copies: 4 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

+
Macromolecule #17: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 17 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

+
Macromolecule #18: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 18 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #19: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 19 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 7.4
Details: 30 mM HEPES pH7.4, 25 mM NaCl, 25 mM KCl, 3% (v/v) glycerol, 5 mM MgCl2 2 mM ATP and 0.5 mM TCEP
GridModel: UltrAuFoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: GOLD / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Details: 25 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15623
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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