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- PDB-6msk: Cryo-EM structures and dynamics of substrate-engaged human 26S pr... -

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Basic information

Entry
Database: PDB / ID: 6msk
TitleCryo-EM structures and dynamics of substrate-engaged human 26S proteasome
Components
  • (26S proteasome non-ATPase regulatory subunit ...) x 11
  • (26S proteasome regulatory subunit ...) x 5
  • (Proteasome subunit alpha type- ...) x 7
  • (Proteasome subunit beta type- ...) x 7
  • 26S proteasome complex subunit SEM1Proteasome
  • Rpt2, NP_002793.2 (26SHA chain B)
  • substrate
KeywordsHYDROLASE / Proteosome
Function / homology
Function and homology information


modulation by host of viral transcription / purine ribonucleoside triphosphate binding / thyrotropin-releasing hormone receptor binding / positive regulation of inclusion body assembly / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / proteasome accessory complex / meiosis I / nuclear proteasome complex / proteasome regulatory particle / proteasome-activating activity ...modulation by host of viral transcription / purine ribonucleoside triphosphate binding / thyrotropin-releasing hormone receptor binding / positive regulation of inclusion body assembly / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / proteasome accessory complex / meiosis I / nuclear proteasome complex / proteasome regulatory particle / proteasome-activating activity / proteasome regulatory particle, lid subcomplex / regulation of endopeptidase activity / proteasome regulatory particle, base subcomplex / Lys63-specific deubiquitinase activity / cytosolic proteasome complex / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / negative regulation of programmed cell death / myofibril / proteasome binding / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / regulation of protein catabolic process / polyubiquitin modification-dependent protein binding / negative regulation of G2/M transition of mitotic cell cycle / proteasome storage granule / NIK/NF-kappaB signaling / Wnt signaling pathway, planar cell polarity pathway / proteasomal ubiquitin-independent protein catabolic process / endopeptidase activator activity / proteasome core complex / isopeptidase activity / regulation of hematopoietic stem cell differentiation / proteasome complex / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / regulation of mitotic cell cycle phase transition / proteasome core complex, alpha-subunit complex / regulation of cellular amino acid metabolic process / proteasome assembly / NF-kappaB binding / threonine-type endopeptidase activity / stem cell differentiation / polysome / ciliary basal body / sarcomere / ubiquitin-dependent ERAD pathway / inclusion body / mRNA export from nucleus / response to organonitrogen compound / proteolysis involved in cellular protein catabolic process / regulation of proteasomal protein catabolic process / enzyme regulator activity / TBP-class protein binding / Regulation of activated PAK-2p34 by proteasome mediated degradation / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / CDT1 association with the CDC6:ORC:origin complex / Degradation of DVL / pre-replicative complex assembly / Autodegradation of Cdh1 by Cdh1:APC/C / Asymmetric localization of PCP proteins / APC/C:Cdc20 mediated degradation of Securin / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / positive regulation of RNA polymerase II transcription preinitiation complex assembly / Ubiquitin-dependent degradation of Cyclin D / Vif-mediated degradation of APOBEC3G / Vpu mediated degradation of CD4 / AUF1 (hnRNP D0) binds and destabilizes mRNA / Degradation of GLI1 by the proteasome / Hh mutants are degraded by ERAD / TNFR2 non-canonical NF-kB pathway / Negative regulation of NOTCH4 signaling / Defective CFTR causes cystic fibrosis / Hedgehog ligand biogenesis / Dectin-1 mediated noncanonical NF-kB signaling / Hedgehog 'on' state / P-body / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / modulation of chemical synaptic transmission / GLI3 is processed to GLI3R by the proteasome / Degradation of GLI2 by the proteasome / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Activation of NF-kappaB in B cells / cytoplasmic ribonucleoprotein granule / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of AXIN / G2/M Checkpoints / tumor necrosis factor-mediated signaling pathway / negative regulation of neuron death / ABC-family proteins mediated transport / Degradation of beta-catenin by the destruction complex / Autodegradation of the E3 ubiquitin ligase COP1 / response to virus / Metalloprotease DUBs / Regulation of RUNX3 expression and activity / lipopolysaccharide binding / Regulation of expression of SLITs and ROBOs / double-strand break repair via homologous recombination / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1
Similarity search - Function
HEAT repeats / 26S Proteasome non-ATPase regulatory subunit 11 / 26S Proteasome regulatory subunit 4 / 26S proteasome regulatory subunit 10B / Proteasome subunit beta 6 / Proteasome subunit alpha 7 / Ubiquitin interaction motif / Proteasome regulatory subunit C-terminal / 26S proteasome non-ATPase regulatory subunit 3 / 26S Proteasome non-ATPase regulatory subunit 6 ...HEAT repeats / 26S Proteasome non-ATPase regulatory subunit 11 / 26S Proteasome regulatory subunit 4 / 26S proteasome regulatory subunit 10B / Proteasome subunit beta 6 / Proteasome subunit alpha 7 / Ubiquitin interaction motif / Proteasome regulatory subunit C-terminal / 26S proteasome non-ATPase regulatory subunit 3 / 26S Proteasome non-ATPase regulatory subunit 6 / 26S proteasome regulatory subunit, C-terminal / 26S proteasome non-ATPase regulatory subunit Rpn12 / DSS1/SEM1 family / 26S Proteasome non-ATPase regulatory subunit 12 / 26S proteasome regulatory subunit RPN5 C-terminal domain / DSS1_SEM1 / DSS1/SEM1 / 26S proteasome regulatory subunit RPN5, C-terminal domain / 6S proteasome subunit Rpn6, C-terminal helix domain / 26S proteasome subunit RPN6 C-terminal helix domain / 26S proteasome regulatory subunit RPN6 N-terminal domain / 26S proteasome regulatory subunit Rpn6, N-terminal / 26S Proteasome non-ATPase regulatory subunit 1 / 26S proteasome regulatory subunit RPN2 C-terminal domain / 26S proteasome regulatory subunit RPN2, C-terminal / 26S Proteasome non-ATPase regulatory subunit 13 / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / 26S Proteasome non-ATPase regulatory subunit 7/8 / 26S Proteasome non-ATPase regulatory subunit 14 / 26S proteasome non-ATPase regulatory subunit RPN1, C-terminal / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / 26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / RPN1 N-terminal domain / RPN1, N-terminal / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 26S proteasome subunit RPN7 / 26S Proteasome regulatory subunit 6A / 26S Proteasome regulatory subunit 7 / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / Proteasome/cyclosome repeat / 26S Proteasome regulatory subunit 6B / Proteasome/cyclosome repeat / von Willebrand factor type A domain / Ubiquitin-interacting motif. / CSN8/PSMD8/EIF3K family / CSN8/PSMD8/EIF3K / 26S proteasome regulatory subunit P45-like / Proteasomal ATPase OB C-terminal domain / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / Proteasomal ATPase OB C-terminal domain / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / PCI domain profile. / Proteasome component (PCI) domain / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Proteasome subunit beta 5 / Proteasome subunit beta 7 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / von Willebrand factor (vWF) type A domain / Proteasome subunit beta 1 / Proteasome beta 3 subunit / Proteasome subunit beta 2 / Proteasome subunit alpha 1 / Proteasome subunit alpha4 / Proteasome subunit alpha2 / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome subunit alpha 3 / VWFA domain profile. / 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. / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / Proteasome subunit A N-terminal signature Add an annotation / Proteasome alpha-subunit, N-terminal domain / von Willebrand factor, type A / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / AAA+ lid domain / MPN domain profile. / AAA ATPase, AAA+ lid domain / MPN domain / Proteasome beta-type subunit profile. / Proteasome B-type subunit / Proteasome subunit / Proteasome, subunit alpha/beta / AAA-protein family signature. / ATPase, AAA-type, conserved site / von Willebrand factor A-like domain superfamily / Nucleophile aminohydrolases, N-terminal / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core
Similarity search - Domain/homology
26S proteasome non-ATPase regulatory subunit 4 / 26S proteasome non-ATPase regulatory subunit 7 / 26S proteasome non-ATPase regulatory subunit 8 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 / Proteasome subunit alpha type-6 / 26S proteasome complex subunit SEM1 / Proteasome subunit beta type-7 / 26S proteasome regulatory subunit 4 / 26S proteasome regulatory subunit 8 ...26S proteasome non-ATPase regulatory subunit 4 / 26S proteasome non-ATPase regulatory subunit 7 / 26S proteasome non-ATPase regulatory subunit 8 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 / Proteasome subunit alpha type-6 / 26S proteasome complex subunit SEM1 / Proteasome subunit beta type-7 / 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 / 26S proteasome regulatory subunit 7 / 26S proteasome non-ATPase regulatory subunit 1 / 26S proteasome regulatory subunit 6B / ADENOSINE-5'-DIPHOSPHATE / Proteasome subunit beta type-5 / 26S proteasome non-ATPase regulatory subunit 3 / ADENOSINE-5'-TRIPHOSPHATE / 26S proteasome regulatory subunit 10B / 26S proteasome non-ATPase regulatory subunit 11 / 26S proteasome non-ATPase regulatory subunit 12 / 26S proteasome non-ATPase regulatory subunit 14 / Proteasome subunit alpha type-7 / 26S proteasome regulatory subunit 6A / Proteasome subunit beta type-6 / 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 / 26S proteasome non-ATPase regulatory subunit 13
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae RM11-1a (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsMao, Y.D.
Funding support China, United States, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)11774012 China
National Natural Science Foundation of China (NSFC)91530321 China
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM43601 United States
CitationJournal: Nature / Year: 2019
Title: Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome.
Authors: Yuanchen Dong / Shuwen Zhang / Zhaolong Wu / Xuemei Li / Wei Li Wang / Yanan Zhu / Svetla Stoilova-McPhie / Ying Lu / Daniel Finley / Youdong Mao /
Abstract: The proteasome is an ATP-dependent, 2.5-megadalton molecular machine that is responsible for selective protein degradation in eukaryotic cells. Here we present cryo-electron microscopy structures of ...The proteasome is an ATP-dependent, 2.5-megadalton molecular machine that is responsible for selective protein degradation in eukaryotic cells. Here we present cryo-electron microscopy structures of the substrate-engaged human proteasome in seven conformational states at 2.8-3.6 Å resolution, captured during breakdown of a polyubiquitylated protein. These structures illuminate a spatiotemporal continuum of dynamic substrate-proteasome interactions from ubiquitin recognition to substrate translocation, during which ATP hydrolysis sequentially navigates through all six ATPases. There are three principal modes of coordinated hydrolysis, featuring hydrolytic events in two oppositely positioned ATPases, in two adjacent ATPases and in one ATPase at a time. These hydrolytic modes regulate deubiquitylation, initiation of translocation and processive unfolding of substrates, respectively. Hydrolysis of ATP powers a hinge-like motion in each ATPase that regulates its substrate interaction. Synchronization of ATP binding, ADP release and ATP hydrolysis in three adjacent ATPases drives rigid-body rotations of substrate-bound ATPases that are propagated unidirectionally in the ATPase ring and unfold the substrate.
History
DepositionOct 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

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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
b: 26S proteasome non-ATPase regulatory subunit 4
c: 26S proteasome non-ATPase regulatory subunit 14
d: 26S proteasome non-ATPase regulatory subunit 8
e: 26S proteasome complex subunit SEM1
f: 26S proteasome non-ATPase regulatory subunit 2
A: 26S proteasome regulatory subunit 7
B: Rpt2, NP_002793.2 (26SHA chain B)
C: 26S proteasome regulatory subunit 8
D: 26S proteasome regulatory subunit 6B
E: 26S proteasome regulatory subunit 10B
F: 26S proteasome regulatory subunit 6A
v: substrate
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: 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: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,665,24058
Polymers1,662,59847
Non-polymers2,64311
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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

#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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD1 / Production host: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD3 / Production host: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD12 / Production host: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD11 / Production host: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD6, KIAA0107, PFAAP4 / Production host: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD7, MOV34L / Production host: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD13 / Production host: Homo sapiens (human) / References: UniProt: Q9UNM6
#8: 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 / ASF / Multiubiquitin chain-binding protein


Mass: 40781.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD4, MCB1 / Production host: Homo sapiens (human) / References: UniProt: P55036
#9: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD14, POH1 / Production host: Homo sapiens (human)
References: UniProt: O00487, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases
#10: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD8 / Production host: Homo sapiens (human) / References: UniProt: P48556
#12: 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: 98425.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD2, TRAP2 / Production host: Homo sapiens (human) / References: UniProt: Q13200

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Protein , 2 types, 2 molecules eB

#11: Protein 26S proteasome complex subunit SEM1 / Proteasome / 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEM1, C7orf76, DSS1, SHFDG1, SHFM1 / Production host: Homo sapiens (human) / References: UniProt: P60896
#14: Protein Rpt2, NP_002793.2 (26SHA chain B)


Mass: 49260.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: P62191

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

#13: Protein 26S proteasome regulatory subunit 7 / 26S proteasome AAA-ATPase subunit RPT1 / Proteasome 26S subunit ATPase 2 / Protein MSS1


Mass: 48700.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMC2, MSS1 / Production host: Homo sapiens (human) / References: UniProt: P35998
#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: 44852.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMC5, SUG1 / Production host: Homo sapiens (human) / References: UniProt: P62195
#16: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMC4, MIP224, TBP7 / Production host: Homo sapiens (human) / References: UniProt: P43686
#17: Protein 26S proteasome regulatory subunit 10B


Mass: 45867.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMC6 / Production host: Homo sapiens (human) / References: UniProt: A0A087X2I1, UniProt: P62333*PLUS
#18: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMC3, TBP1 / Production host: Homo sapiens (human) / References: UniProt: P17980

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Protein/peptide , 1 types, 1 molecules v

#19: Protein/peptide substrate


Mass: 3081.790 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae RM11-1a (yeast)
Production host: Escherichia coli K-12 (bacteria)

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

#20: Protein Proteasome subunit alpha type-6 / / 27 kDa prosomal protein / p27K / Macropain iota chain / Multicatalytic endopeptidase complex iota ...27 kDa prosomal protein / p27K / Macropain iota chain / Multicatalytic endopeptidase complex iota chain / Proteasome iota chain


Mass: 27301.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA6, PROS27 / Production host: Homo sapiens (human)
References: UniProt: P60900, proteasome endopeptidase complex
#21: Protein Proteasome subunit alpha type-2 / / Macropain subunit C3 / Multicatalytic endopeptidase complex subunit C3 / Proteasome component C3


Mass: 25796.338 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA2, HC3, PSC3 / Production host: Homo sapiens (human)
References: UniProt: P25787, proteasome endopeptidase complex
#22: 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


Mass: 29394.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA4, HC9, PSC9 / Production host: Homo sapiens (human)
References: UniProt: P25789, proteasome endopeptidase complex
#23: Protein Proteasome subunit alpha type-7 / / Proteasome subunit RC6-1 / Proteasome subunit XAPC7


Mass: 27798.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA7, HSPC / Production host: Homo sapiens (human)
References: UniProt: O14818, proteasome endopeptidase complex
#24: Protein Proteasome subunit alpha type-5 / / Macropain zeta chain / Multicatalytic endopeptidase complex zeta chain / Proteasome zeta chain


Mass: 26304.779 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA5 / Production host: Homo sapiens (human)
References: UniProt: P28066, proteasome endopeptidase complex
#25: 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


Mass: 30150.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA1, HC2, NU, PROS30, PSC2 / Production host: Homo sapiens (human)
References: UniProt: P25786, proteasome endopeptidase complex
#26: Protein Proteasome subunit alpha type-3 / / Macropain subunit C8 / Multicatalytic endopeptidase complex subunit C8 / Proteasome component C8


Mass: 28338.057 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA3, HC8, PSC8 / Production host: Homo sapiens (human)
References: UniProt: P25788, proteasome endopeptidase complex

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

#27: 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


Mass: 25246.455 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMB6, LMPY, Y / Production host: Homo sapiens (human)
References: UniProt: P28072, proteasome endopeptidase complex
#28: Protein Proteasome subunit beta type-7 / / Macropain chain Z / Multicatalytic endopeptidase complex chain Z / Proteasome subunit Z


Mass: 29869.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMB7, Z / Production host: Homo sapiens (human)
References: UniProt: Q99436, proteasome endopeptidase complex
#29: Protein Proteasome subunit beta type-3 / PSMB3 / Proteasome chain 13 / Proteasome component C10-II / Proteasome theta chain


Mass: 22841.701 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMB3 / Production host: Homo sapiens (human)
References: UniProt: P49720, proteasome endopeptidase complex
#30: Protein Proteasome subunit beta type-2 / PSMB2 / Macropain subunit C7-I / Multicatalytic endopeptidase complex subunit C7-I / Proteasome component C7-I


Mass: 22864.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMB2 / Production host: Homo sapiens (human)
References: UniProt: P49721, proteasome endopeptidase complex
#31: Protein Proteasome subunit beta type-5 / PSMB5 / 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


Mass: 28379.053 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMB5, LMPX, MB1, X / Production host: Homo sapiens (human)
References: UniProt: P28074, proteasome endopeptidase complex
#32: Protein Proteasome subunit beta type-1 / PSMB1 / 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


Mass: 26391.201 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMB1, PSC5 / Production host: Homo sapiens (human)
References: UniProt: P20618, proteasome endopeptidase complex
#33: Protein Proteasome subunit beta type-4 / PSMB4 / 26 kDa prosomal protein / PROS-26 / Macropain beta chain / Multicatalytic endopeptidase complex ...26 kDa prosomal protein / PROS-26 / Macropain beta chain / Multicatalytic endopeptidase complex beta chain / Proteasome beta chain / Proteasome chain 3 / HsN3


Mass: 29099.986 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMB4, PROS26 / Production host: Homo sapiens (human)
References: UniProt: P28070, proteasome endopeptidase complex

+
Non-polymers , 4 types, 11 molecules

#34: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#35: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


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


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#37: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Experimental details

-
Experiment

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

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Sample preparation

ComponentName: Proteasome / Type: COMPLEX / Entity ID: #1-#8, #10-#13, #16-#32 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 44 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 348646 / Symmetry type: POINT

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