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- PDB-22mm: Structure of human 26S proteasome complexed with midnolin(1-111+3... -

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Basic information

Entry
Database: PDB / ID: 22mm
TitleStructure of human 26S proteasome complexed with midnolin(1-111+337-468)
Components
  • (26S proteasome non-ATPase regulatory subunit ...) x 10
  • (26S proteasome regulatory subunit ...) x 5
  • (Proteasome subunit alpha type- ...) x 7
  • (Proteasome subunit beta type- ...) x 7
  • 26S proteasome complex subunit SEM1
  • Isoform Long of Proteasome subunit alpha type-1
  • Midnolin,MCHERRY,fusion tag
  • Proteasome 26S subunit, ATPase 6
KeywordsHYDROLASE / 26S proteasome / midnolin
Function / homology
Function and homology information


negative regulation of glucokinase activity / thyrotropin-releasing hormone receptor binding / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / nuclear proteasome complex / host-mediated perturbation of viral transcription / positive regulation of inclusion body assembly / integrator complex / proteasome accessory complex / meiosis I ...negative regulation of glucokinase activity / thyrotropin-releasing hormone receptor binding / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / nuclear proteasome complex / host-mediated perturbation of viral transcription / positive regulation of inclusion body assembly / integrator complex / proteasome accessory complex / meiosis I / 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 / Regulation of ornithine decarboxylase (ODC) / metal-dependent deubiquitinase activity / perinuclear theca / Proteasome assembly / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / K63-linked deubiquitinase activity / 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) / transcription factor binding / 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 / Presynaptic phase of homologous DNA pairing and strand exchange / general transcription initiation factor binding / protein deubiquitination / blastocyst development / immune system process / NF-kappaB binding / proteasome endopeptidase complex / 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 / enzyme regulator activity / regulation of proteasomal protein catabolic process / inclusion body / ciliary tip / : / proteasome complex / TBP-class protein binding / bioluminescence / stem cell differentiation / sarcomere / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / ubiquitin binding / generation of precursor metabolites and energy / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / sperm end piece / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / centriole / negative regulation of inflammatory response to antigenic stimulus / P-body / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Degradation of DVL / lipopolysaccharide binding / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of CRY and PER proteins / Degradation of AXIN / Hh mutants are degraded by ERAD / Activation of NF-kappaB in B cells / G2/M Checkpoints / Hedgehog ligand biogenesis / Degradation of GLI1 by the proteasome / Defective CFTR causes cystic fibrosis / Autodegradation of the E3 ubiquitin ligase COP1 / Regulation of RUNX3 expression and activity / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling
Similarity search - Function
Midnolin / : / : / 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 / : ...Midnolin / : / : / 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 / 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 / Proteasome/cyclosome repeat / : / 26S proteasome regulatory subunit 7, OB domain / Proteasome/cyclosome repeat / : / : / : / 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 / PCI/PINT associated module / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / 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. / 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. / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / AAA ATPase, AAA+ lid domain / AAA+ lid domain / MPN domain profile. / Green fluorescent protein, GFP / ATPase, AAA-type, conserved site / AAA-protein family signature. / Nucleophile aminohydrolases, N-terminal / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Armadillo-like helical / Ubiquitin family / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
N-[(BENZYLOXY)CARBONYL]-L-LEUCYL-N-[(2S)-4-METHYL-1-OXOPENTAN-2-YL]-L-LEUCINAMIDE / ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Chem-LDZ / 26S proteasome regulatory subunit 10B / MCHERRY / 26S proteasome non-ATPase regulatory subunit 11 / 26S proteasome non-ATPase regulatory subunit 12 / Ubiquitin C-terminal hydrolase PSMD14 / Proteasome subunit alpha type-7 ...N-[(BENZYLOXY)CARBONYL]-L-LEUCYL-N-[(2S)-4-METHYL-1-OXOPENTAN-2-YL]-L-LEUCINAMIDE / ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Chem-LDZ / 26S proteasome regulatory subunit 10B / MCHERRY / 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 complex subunit SEM1 / Proteasome subunit alpha type-6 / 26S proteasome regulatory subunit 4 / 26S proteasome regulatory subunit 8 / 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)
Escherichia coli str. K-12 substr. MG1655 (bacteria)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsLiang, L. / Zhu, C. / Qin, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171224 China
CitationJournal: To Be Published
Title: Structural dynamics of the midnolin-proteasome during ubiquitin-independent substrate turnover
Authors: Zhu, C. / Qin, L. / Liang, L.
History
DepositionJan 16, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 1, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.0Apr 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)1,676,13564
Polymers1,670,21146
Non-polymers5,92418
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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26S proteasome non-ATPase regulatory subunit ... , 10 types, 10 molecules UVWXYZacdu

#1: 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
#2: Protein 26S proteasome non-ATPase regulatory subunit 3 / 26S proteasome regulatory subunit RPN3 / 26S proteasome regulatory subunit S3 / Proteasome subunit p58


Mass: 60935.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43242
#3: 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
#4: 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
#5: 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
#6: 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
#7: 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
#8: Protein 26S proteasome non-ATPase regulatory subunit 14 / 26S proteasome regulatory subunit RPN11 / 26S proteasome-associated PAD1 homolog 1


Mass: 34488.824 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
#9: Protein 26S proteasome non-ATPase regulatory subunit 8 / 26S proteasome regulatory subunit RPN12 / 26S proteasome regulatory subunit S14 / p31


Mass: 39536.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P48556
#33: 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

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Protein , 4 types, 5 molecules eELlf

#10: 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
#15: Protein Proteasome 26S subunit, ATPase 6 / 26S proteasome regulatory subunit 10B


Mass: 45867.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A087X2I1
#22: Protein Isoform Long of 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: 30150.277 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25786
#32: Protein Midnolin,MCHERRY,fusion tag / Midbrain nucleolar protein


Mass: 49195.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Midnolin-mCherry, midnolin(1-111+337-468)
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria), (gene. exp.) synthetic construct (others)
Gene: MIDN, mCherry / Production host: Homo sapiens (human) / References: UniProt: Q504T8, UniProt: A0A4D6FVK6

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26S proteasome regulatory subunit ... , 5 types, 5 molecules ABCDF

#11: 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
#12: 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
#13: 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: 44852.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62195
#14: 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
#16: 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

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Proteasome subunit alpha type- ... , 7 types, 12 molecules GgHhIiJKkMmj

#17: 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: 27301.262 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P60900
#18: 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: 25796.338 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25787
#19: 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: 29394.648 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25789
#20: 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.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O14818
#21: 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
#23: 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: 28338.057 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25788
#31: Protein Proteasome subunit alpha type-7 / Proteasome subunit RC6-1 / Proteasome subunit XAPC7 / Proteasome subunit alpha-4 / alpha-4


Mass: 27798.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O14818

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

#24: 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: 25246.455 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P28072, proteasome endopeptidase complex
#25: 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: 29869.223 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q99436, proteasome endopeptidase complex
#26: 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: 22841.701 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P49720
#27: 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
#28: 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: 28379.053 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P28074, proteasome endopeptidase complex
#29: 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: 26391.201 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P20618
#30: 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: 29099.986 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P28070

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Non-polymers , 5 types, 18 molecules

#34: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#35: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#36: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#37: 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
#38: Chemical
ChemComp-LDZ / N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-4-methyl-1-oxopentan-2-yl]-L-leucinamide


Type: Peptide-like / Class: Inhibitor / Mass: 475.621 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C26H41N3O5 / Feature type: SUBJECT OF INVESTIGATION
References: N-[(BENZYLOXY)CARBONYL]-L-LEUCYL-N-[(2S)-4-METHYL-1-OXOPENTAN-2-YL]-L-LEUCINAMIDE
Comment: inhibitor*YM

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Details

Has ligand of interestY
Has protein modificationY

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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: 26S proteasome complexed with midnolin delCatch / Type: COMPLEX / Entity ID: #1-#33 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
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: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17418 / Symmetry type: POINT
RefinementHighest resolution: 3.42 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004105027
ELECTRON MICROSCOPYf_angle_d0.826142010
ELECTRON MICROSCOPYf_dihedral_angle_d6.2114473
ELECTRON MICROSCOPYf_chiral_restr0.04716109
ELECTRON MICROSCOPYf_plane_restr0.00618333

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