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- PDB-9ug9: The cryo-EM structure of 26S proteasome-Midnolin complex MB state -

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Basic information

Entry
Database: PDB / ID: 9ug9
TitleThe cryo-EM structure of 26S proteasome-Midnolin complex MB state
Components
  • (26S proteasome non-ATPase regulatory subunit ...) x 11
  • (26S proteasome regulatory subunit ...) x 6
  • (Proteasome subunit alpha type- ...) x 7
  • (Proteasome subunit beta type- ...) x 7
  • 26S proteasome complex subunit SEM1
  • Midnolin
  • Substrate
KeywordsHYDROLASE / 26S proteasome / complex / Midnolin
Function / homology
Function and homology information


negative regulation of glucokinase activity / thyrotropin-releasing hormone receptor binding / nuclear proteasome complex / host-mediated perturbation of viral transcription / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / positive regulation of inclusion body assembly / proteasome accessory complex / meiosis I / integrator complex ...negative regulation of glucokinase activity / thyrotropin-releasing hormone receptor binding / nuclear proteasome complex / host-mediated perturbation of viral transcription / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / positive regulation of inclusion body assembly / proteasome accessory complex / meiosis I / integrator complex / purine ribonucleoside triphosphate binding / proteasome regulatory particle / cytosolic proteasome complex / 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 / sperm glycocalyx / protein K63-linked deubiquitination / negative regulation of programmed cell death / metal-dependent deubiquitinase activity / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / proteasome core complex / perinuclear theca / Cross-presentation of soluble exogenous antigens (endosomes) / K63-linked deubiquitinase activity / Somitogenesis / transcription factor binding / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / proteasome binding / Impaired BRCA2 binding to RAD51 / myofibril / regulation of protein catabolic process / proteasome storage granule / proteasomal ubiquitin-independent protein catabolic process / sperm head-tail coupling apparatus / positive regulation of RNA polymerase II transcription preinitiation complex assembly / general transcription initiation factor binding / Presynaptic phase of homologous DNA pairing and strand exchange / blastocyst development / protein deubiquitination / polyubiquitin modification-dependent protein binding / immune system process / proteasome endopeptidase complex / NF-kappaB binding / proteasome core complex, beta-subunit complex / endopeptidase activator activity / threonine-type endopeptidase activity / proteasome assembly / mRNA export from nucleus / proteasome core complex, alpha-subunit complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / enzyme regulator activity / ERAD pathway / regulation of proteasomal protein catabolic process / inclusion body / TBP-class protein binding / : / ciliary tip / proteasome complex / stem cell differentiation / sarcomere / Regulation of activated PAK-2p34 by proteasome mediated degradation / ubiquitin binding / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins / centriole / Ubiquitin-dependent degradation of Cyclin D / sperm end piece / negative regulation of inflammatory response to antigenic stimulus / P-body / 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 / lipopolysaccharide binding / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / 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 / 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 / Regulation of RUNX3 expression and activity / Autodegradation of the E3 ubiquitin ligase COP1 / Defective CFTR causes cystic fibrosis
Similarity search - Function
Midnolin / : / Ubiquitin interaction motif / : / : / 26S proteasome regulatory subunit RPN7/PSMD6 C-terminal helix / PSMD3-like, N-terminal TPR repeats / 26S proteasome non-ATPase regulatory subunit Rpn12 / 26S proteasome regulatory subunit, C-terminal / Proteasome regulatory subunit C-terminal ...Midnolin / : / Ubiquitin interaction motif / : / : / 26S proteasome regulatory subunit RPN7/PSMD6 C-terminal helix / PSMD3-like, N-terminal TPR repeats / 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 / PSD13 N-terminal repeats / 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 subunit RPN2, N-terminal domain / 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 / Proteasome subunit Rpn10 / 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 RPN11 C-terminal domain / DSS1/SEM1 / DSS1/SEM1 family / DSS1_SEM1 / Ubiquitin-interacting motif. / Proteasome/cyclosome repeat / : / 26S proteasome regulatory subunit 7, OB domain / Proteasome/cyclosome repeat / von Willebrand factor type A domain / : / : / : / PSMD12/CSN4, N-terminal / 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 / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / PCI/PINT associated module / HEAT repeats / Proteasome subunit alpha 1 / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / 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 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. / VWFA domain profile. / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / von Willebrand factor (vWF) type A domain / Proteasome subunit / Proteasome, subunit alpha/beta / von Willebrand factor, type A / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature.
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / 26S proteasome non-ATPase regulatory subunit 11 / 26S proteasome non-ATPase regulatory subunit 12 / Ubiquitin C-terminal hydrolase PSMD14 / Proteasome subunit alpha type-7 / 26S proteasome non-ATPase regulatory subunit 3 / 26S proteasome regulatory subunit 6A / Proteasome subunit beta type-1 / Proteasome subunit alpha type-1 ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / 26S proteasome non-ATPase regulatory subunit 11 / 26S proteasome non-ATPase regulatory subunit 12 / Ubiquitin C-terminal hydrolase PSMD14 / Proteasome subunit alpha type-7 / 26S proteasome non-ATPase regulatory subunit 3 / 26S proteasome regulatory subunit 6A / Proteasome subunit beta type-1 / 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 / Proteasome subunit beta type-4 / Proteasome subunit beta type-6 / Proteasome subunit beta type-5 / 26S proteasome regulatory subunit 7 / 26S proteasome regulatory subunit 6B / 26S proteasome non-ATPase regulatory subunit 8 / Proteasome subunit beta type-3 / Proteasome subunit beta type-2 / 26S proteasome non-ATPase regulatory subunit 7 / 26S proteasome non-ATPase regulatory subunit 4 / 26S proteasome complex subunit SEM1 / Proteasome subunit alpha type-6 / 26S proteasome regulatory subunit 4 / 26S proteasome regulatory subunit 8 / 26S proteasome regulatory subunit 10B / 26S proteasome non-ATPase regulatory subunit 2 / 26S proteasome non-ATPase regulatory subunit 6 / Midnolin / Proteasome subunit beta type-7 / 26S proteasome non-ATPase regulatory subunit 1 / 26S proteasome non-ATPase regulatory subunit 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsWang, H.Y. / Xu, W.Q.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32000862 China
Other governmentBX20200351
Other government24ZR1451800
Other government2021kf01
CitationJournal: To Be Published
Title: The cryo-EM structure of 26S proteasome-Midnolin complex MB state
Authors: Wang, H.Y. / Xu, W.Q.
History
DepositionApr 11, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
u: Midnolin
d: 26S proteasome non-ATPase regulatory subunit 8
m: Proteasome subunit alpha type-3
R: Proteasome subunit beta type-5
n: Proteasome subunit beta type-6
E: 26S proteasome regulatory subunit 10B
B: 26S proteasome regulatory subunit 4
e: 26S proteasome complex subunit SEM1
o: Proteasome subunit beta type-7
S: Proteasome subunit beta type-1
D: 26S proteasome regulatory subunit 6B
F: 26S proteasome regulatory subunit 6A
p: Proteasome subunit beta type-3
U: 26S proteasome non-ATPase regulatory subunit 1
C: 26S proteasome regulatory subunit 8
G: Proteasome subunit alpha type-6
q: Proteasome subunit beta type-2
A: 26S proteasome regulatory subunit 7
r: Proteasome subunit beta type-5
V: 26S proteasome non-ATPase regulatory subunit 3
s: Proteasome subunit beta type-1
T: Proteasome subunit beta type-4
v: Substrate
W: 26S proteasome non-ATPase regulatory subunit 12
t: Proteasome subunit beta type-4
H: Proteasome subunit alpha type-2
f: 26S proteasome non-ATPase regulatory subunit 2
X: 26S proteasome non-ATPase regulatory subunit 11
g: Proteasome subunit alpha type-6
I: Proteasome subunit alpha type-4
h: Proteasome subunit alpha type-2
Y: 26S proteasome non-ATPase regulatory subunit 6
M: Proteasome subunit alpha type-3
J: Proteasome subunit alpha type-7
i: Proteasome subunit alpha type-4
Z: 26S proteasome non-ATPase regulatory subunit 7
N: Proteasome subunit beta type-6
K: Proteasome subunit alpha type-5
j: Proteasome subunit alpha type-7
a: 26S proteasome non-ATPase regulatory subunit 13
O: Proteasome subunit beta type-7
L: Proteasome subunit alpha type-1
P: Proteasome subunit beta type-3
b: 26S proteasome non-ATPase regulatory subunit 4
Q: Proteasome subunit beta type-2
k: Proteasome subunit alpha type-5
c: 26S proteasome non-ATPase regulatory subunit 14
l: Proteasome subunit alpha type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,718,86554
Polymers1,716,42448
Non-polymers2,4416
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 2 molecules ue

#1: Protein Midnolin / Midbrain nucleolar protein


Mass: 52076.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MIDN / Production host: Homo sapiens (human) / References: UniProt: Q504T8
#8: Protein 26S proteasome complex subunit SEM1 / 26S proteasome complex subunit DSS1 / Deleted in split hand/split foot protein 1 / Split hand/foot ...26S proteasome complex subunit DSS1 / Deleted in split hand/split foot protein 1 / Split hand/foot deleted protein 1 / Split hand/foot malformation type 1 protein


Mass: 8284.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P60896

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26S proteasome non-ATPase regulatory subunit ... , 11 types, 11 molecules dUVWfXYZabc

#2: Protein 26S proteasome non-ATPase regulatory subunit 8 / 26S proteasome regulatory subunit RPN12 / 26S proteasome regulatory subunit S14 / p31


Mass: 39667.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P48556
#14: Protein 26S proteasome non-ATPase regulatory subunit 1 / 26S proteasome regulatory subunit RPN2 / 26S proteasome regulatory subunit S1 / 26S proteasome subunit p112


Mass: 105958.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q99460
#19: Protein 26S proteasome non-ATPase regulatory subunit 3 / 26S proteasome regulatory subunit RPN3 / 26S proteasome regulatory subunit S3 / Proteasome subunit p58


Mass: 61066.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43242
#22: Protein 26S proteasome non-ATPase regulatory subunit 12 / 26S proteasome regulatory subunit RPN5 / 26S proteasome regulatory subunit p55


Mass: 52979.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O00232
#24: Protein 26S proteasome non-ATPase regulatory subunit 2 / 26S proteasome regulatory subunit RPN1 / 26S proteasome regulatory subunit S2 / 26S proteasome ...26S proteasome regulatory subunit RPN1 / 26S proteasome regulatory subunit S2 / 26S proteasome subunit p97 / Protein 55.11 / Tumor necrosis factor type 1 receptor-associated protein 2


Mass: 100313.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13200
#25: Protein 26S proteasome non-ATPase regulatory subunit 11 / 26S proteasome regulatory subunit RPN6 / 26S proteasome regulatory subunit S9 / 26S proteasome ...26S proteasome regulatory subunit RPN6 / 26S proteasome regulatory subunit S9 / 26S proteasome regulatory subunit p44.5


Mass: 47526.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O00231
#27: Protein 26S proteasome non-ATPase regulatory subunit 6 / 26S proteasome regulatory subunit RPN7 / 26S proteasome regulatory subunit S10 / Breast cancer- ...26S proteasome regulatory subunit RPN7 / 26S proteasome regulatory subunit S10 / Breast cancer-associated protein SGA-113M / Phosphonoformate immuno-associated protein 4 / Proteasome regulatory particle subunit p44S10 / p42A


Mass: 45592.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15008
#29: Protein 26S proteasome non-ATPase regulatory subunit 7 / 26S proteasome regulatory subunit RPN8 / 26S proteasome regulatory subunit S12 / Mov34 protein ...26S proteasome regulatory subunit RPN8 / 26S proteasome regulatory subunit S12 / Mov34 protein homolog / Proteasome subunit p40


Mass: 37086.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P51665
#31: Protein 26S proteasome non-ATPase regulatory subunit 13 / 26S proteasome regulatory subunit RPN9 / 26S proteasome regulatory subunit S11 / 26S proteasome ...26S proteasome regulatory subunit RPN9 / 26S proteasome regulatory subunit S11 / 26S proteasome regulatory subunit p40.5


Mass: 42995.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UNM6
#33: Protein 26S proteasome non-ATPase regulatory subunit 4 / 26S proteasome regulatory subunit RPN10 / 26S proteasome regulatory subunit S5A / Antisecretory ...26S proteasome regulatory subunit RPN10 / 26S proteasome regulatory subunit S5A / Antisecretory factor 1 / AF / ASF / Multiubiquitin chain-binding protein


Mass: 40781.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P55036
#34: Protein 26S proteasome non-ATPase regulatory subunit 14 / 26S proteasome regulatory subunit RPN11 / 26S proteasome-associated PAD1 homolog 1


Mass: 34620.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: O00487, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases

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Proteasome subunit alpha type- ... , 7 types, 14 molecules mMGgHhIiJjKkLl

#3: Protein Proteasome subunit alpha type-3 / Macropain subunit C8 / Multicatalytic endopeptidase complex subunit C8 / Proteasome component C8 / ...Macropain subunit C8 / Multicatalytic endopeptidase complex subunit C8 / Proteasome component C8 / Proteasome subunit alpha-7 / alpha-7


Mass: 28469.252 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25788
#16: Protein Proteasome subunit alpha type-6 / 27 kDa prosomal protein / PROS-27 / p27K / Macropain iota chain / Multicatalytic endopeptidase ...27 kDa prosomal protein / PROS-27 / p27K / Macropain iota chain / Multicatalytic endopeptidase complex iota chain / Proteasome iota chain / Proteasome subunit alpha-1 / alpha-1


Mass: 27432.459 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P60900
#23: Protein Proteasome subunit alpha type-2 / Macropain subunit C3 / Multicatalytic endopeptidase complex subunit C3 / Proteasome component C3 / ...Macropain subunit C3 / Multicatalytic endopeptidase complex subunit C3 / Proteasome component C3 / Proteasome subunit alpha-2 / alpha-2


Mass: 25927.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25787
#26: Protein Proteasome subunit alpha type-4 / Macropain subunit C9 / Multicatalytic endopeptidase complex subunit C9 / Proteasome component C9 / ...Macropain subunit C9 / Multicatalytic endopeptidase complex subunit C9 / Proteasome component C9 / Proteasome subunit L / Proteasome subunit alpha-3 / alpha-3


Mass: 29525.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25789
#28: Protein Proteasome subunit alpha type-7 / Proteasome subunit RC6-1 / Proteasome subunit XAPC7 / Proteasome subunit alpha-4 / alpha-4


Mass: 27929.891 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O14818
#30: Protein Proteasome subunit alpha type-5 / Macropain zeta chain / Multicatalytic endopeptidase complex zeta chain / Proteasome subunit alpha-5 ...Macropain zeta chain / Multicatalytic endopeptidase complex zeta chain / Proteasome subunit alpha-5 / alpha-5 / Proteasome zeta chain


Mass: 26435.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P28066
#32: Protein Proteasome subunit alpha type-1 / 30 kDa prosomal protein / PROS-30 / Macropain subunit C2 / Multicatalytic endopeptidase complex ...30 kDa prosomal protein / PROS-30 / Macropain subunit C2 / Multicatalytic endopeptidase complex subunit C2 / Proteasome component C2 / Proteasome nu chain / Proteasome subunit alpha-6 / alpha-6


Mass: 29595.627 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25786

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Proteasome subunit beta type- ... , 7 types, 14 molecules RrnNoOSspPqQTt

#4: Protein Proteasome subunit beta type-5 / Macropain epsilon chain / Multicatalytic endopeptidase complex epsilon chain / Proteasome chain 6 / ...Macropain epsilon chain / Multicatalytic endopeptidase complex epsilon chain / Proteasome chain 6 / Proteasome epsilon chain / Proteasome subunit MB1 / Proteasome subunit X / Proteasome subunit beta-5 / beta-5


Mass: 28510.248 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P28074, proteasome endopeptidase complex
#5: Protein Proteasome subunit beta type-6 / Macropain delta chain / Multicatalytic endopeptidase complex delta chain / Proteasome delta chain / ...Macropain delta chain / Multicatalytic endopeptidase complex delta chain / Proteasome delta chain / Proteasome subunit Y / Proteasome subunit beta-1 / beta-1


Mass: 25377.652 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P28072, proteasome endopeptidase complex
#9: Protein Proteasome subunit beta type-7 / Macropain chain Z / Multicatalytic endopeptidase complex chain Z / Proteasome subunit Z / ...Macropain chain Z / Multicatalytic endopeptidase complex chain Z / Proteasome subunit Z / Proteasome subunit beta-2 / beta-2


Mass: 30000.418 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q99436, proteasome endopeptidase complex
#10: Protein Proteasome subunit beta type-1 / Macropain subunit C5 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / ...Macropain subunit C5 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / Proteasome gamma chain / Proteasome subunit beta-6 / beta-6


Mass: 26522.396 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P20618
#13: Protein Proteasome subunit beta type-3 / Proteasome chain 13 / Proteasome component C10-II / Proteasome subunit beta-3 / beta-3 / Proteasome ...Proteasome chain 13 / Proteasome component C10-II / Proteasome subunit beta-3 / beta-3 / Proteasome theta chain


Mass: 22972.896 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P49720
#17: Protein Proteasome subunit beta type-2 / Macropain subunit C7-I / Multicatalytic endopeptidase complex subunit C7-I / Proteasome component ...Macropain subunit C7-I / Multicatalytic endopeptidase complex subunit C7-I / Proteasome component C7-I / Proteasome subunit beta-4 / beta-4


Mass: 22864.277 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P49721
#20: Protein Proteasome subunit beta type-4 / 26 kDa prosomal protein / HsBPROS26 / PROS-26 / Macropain beta chain / Multicatalytic endopeptidase ...26 kDa prosomal protein / HsBPROS26 / PROS-26 / Macropain beta chain / Multicatalytic endopeptidase complex beta chain / Proteasome beta chain / Proteasome chain 3 / HsN3 / Proteasome subunit beta-7 / beta-7


Mass: 29231.178 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P28070

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26S proteasome regulatory subunit ... , 6 types, 6 molecules EBDFCA

#6: Protein 26S proteasome regulatory subunit 10B / 26S proteasome AAA-ATPase subunit RPT4 / Proteasome 26S subunit ATPase 6 / Proteasome subunit p42


Mass: 44241.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62333
#7: Protein 26S proteasome regulatory subunit 4 / P26s4 / 26S proteasome AAA-ATPase subunit RPT2 / Proteasome 26S subunit ATPase 1


Mass: 49260.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62191
#11: Protein 26S proteasome regulatory subunit 6B / 26S proteasome AAA-ATPase subunit RPT3 / MB67-interacting protein / MIP224 / Proteasome 26S subunit ...26S proteasome AAA-ATPase subunit RPT3 / MB67-interacting protein / MIP224 / Proteasome 26S subunit ATPase 4 / Tat-binding protein 7 / TBP-7


Mass: 47426.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P43686
#12: Protein 26S proteasome regulatory subunit 6A / 26S proteasome AAA-ATPase subunit RPT5 / Proteasome 26S subunit ATPase 3 / Proteasome subunit P50 / ...26S proteasome AAA-ATPase subunit RPT5 / Proteasome 26S subunit ATPase 3 / Proteasome subunit P50 / Tat-binding protein 1 / TBP-1


Mass: 49266.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P17980
#15: Protein 26S proteasome regulatory subunit 8 / 26S proteasome AAA-ATPase subunit RPT6 / Proteasome 26S subunit ATPase 5 / Proteasome subunit p45 / ...26S proteasome AAA-ATPase subunit RPT6 / Proteasome 26S subunit ATPase 5 / Proteasome subunit p45 / Thyroid hormone receptor-interacting protein 1 / TRIP1 / p45/SUG


Mass: 45694.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62195
#18: Protein 26S proteasome regulatory subunit 7 / 26S proteasome AAA-ATPase subunit RPT1 / Proteasome 26S subunit ATPase 2


Mass: 48700.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P35998

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Protein/peptide , 1 types, 1 molecules v

#21: Protein/peptide Substrate


Mass: 1294.587 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: In the process of protein purification, we used Midnolin (Uniprot: Q504T8) to pull down the endogenous 26S proteasome. However, since the 26S proteasome can unfold and proteolytic cleave ...Details: In the process of protein purification, we used Midnolin (Uniprot: Q504T8) to pull down the endogenous 26S proteasome. However, since the 26S proteasome can unfold and proteolytic cleave many endougeous proteins, we are unable to determine which specific segment of these two proteins corresponds to the density of chain v, which appears to be undergoing unfolding within the AAA-ATPase ring. Therefore, we labeled it as UNK.
Source: (natural) Homo sapiens (human)

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Non-polymers , 3 types, 6 molecules

#35: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#36: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#37: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of midnolin and 26S proteasome in MB state / Type: COMPLEX
Entity ID: #8, #14, #19, #22, #25, #27, #29, #31, #33-#34, #2, #7, #11, #15, #6, #12, #21, #24, #18, #3, #5, #9, #13, #17, #4, #10, #16, #20, #23, #26, #28, #30, #32
Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 108120 / Symmetry type: POINT

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