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- PDB-8jri: Cryo-EM structure of human 26S proteasomal RP subcomplex (Ea stat... -

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Basic information

Entry
Database: PDB / ID: 8jri
TitleCryo-EM structure of human 26S proteasomal RP subcomplex (Ea state) without any bound substrate.
Components
  • (26S protease regulatory subunit ...) x 6
  • (26S proteasome non-ATPase regulatory subunit ...) x 11
  • (Proteasome subunit alpha type- ...) x 7
  • 26S proteasome complex subunit DSS1
KeywordsCYTOSOLIC PROTEIN / protein degradation / macromolecular complex / ubiquitin-proteasome system
Function / homology
Function and homology information


positive regulation of inclusion body assembly / thyrotropin-releasing hormone receptor binding / modulation by host of viral transcription / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / cytosolic proteasome complex / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / proteasome accessory complex / integrator complex / purine ribonucleoside triphosphate binding ...positive regulation of inclusion body assembly / thyrotropin-releasing hormone receptor binding / modulation by host of viral transcription / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / cytosolic proteasome complex / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / proteasome accessory complex / integrator complex / purine ribonucleoside triphosphate binding / meiosis I / proteasome regulatory particle / positive regulation of proteasomal protein catabolic process / proteasome-activating activity / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / metal-dependent deubiquitinase activity / negative regulation of programmed cell death / protein K63-linked deubiquitination / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / 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 / Cross-presentation of soluble exogenous antigens (endosomes) / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / proteasome core complex / Resolution of D-loop Structures through Holliday Junction Intermediates / Somitogenesis / K63-linked deubiquitinase activity / Impaired BRCA2 binding to RAD51 / proteasome binding / transcription factor binding / regulation of protein catabolic process / myofibril / proteasome storage granule / Presynaptic phase of homologous DNA pairing and strand exchange / general transcription initiation factor binding / blastocyst development / polyubiquitin modification-dependent protein binding / immune system process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / protein deubiquitination / endopeptidase activator activity / NF-kappaB binding / proteasome assembly / proteasome core complex, alpha-subunit complex / mRNA export from nucleus / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / inclusion body / enzyme regulator activity / ERAD pathway / regulation of proteasomal protein catabolic process / proteasome complex / proteolysis involved in protein catabolic process / sarcomere / Regulation of activated PAK-2p34 by proteasome mediated degradation / 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 / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / stem cell differentiation / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / lipopolysaccharide binding / Degradation of AXIN / Hh mutants are degraded by ERAD / negative regulation of inflammatory response to antigenic stimulus / P-body / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / G2/M Checkpoints / Defective CFTR causes cystic fibrosis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Negative regulation of NOTCH4 signaling / Vif-mediated degradation of APOBEC3G / Regulation of RUNX3 expression and activity / Hedgehog 'on' state / double-strand break repair via homologous recombination / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / MAPK6/MAPK4 signaling / Degradation of beta-catenin by the destruction complex / response to virus / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / ABC-family proteins mediated transport
Similarity search - Function
: / Ubiquitin interaction motif / : / 26S proteasome regulatory subunit RPN7/PSMD6 C-terminal helix / 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 ...: / Ubiquitin interaction motif / : / 26S proteasome regulatory subunit RPN7/PSMD6 C-terminal helix / 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 regulatory subunit RPN11 C-terminal domain / DSS1/SEM1 / Proteasome subunit Rpn10 / 26S Proteasome non-ATPase regulatory subunit 7/8 / DSS1/SEM1 family / DSS1_SEM1 / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / RPN1, N-terminal / 26S proteasome non-ATPase regulatory subunit RPN1, C-terminal / RPN1 N-terminal domain / 26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / : / 26S proteasome regulatory subunit 7, OB domain / : / : / : / 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 / Proteasome/cyclosome repeat / Proteasome/cyclosome repeat / Ubiquitin-interacting motif. / PCI/PINT associated module / : / von Willebrand factor type A domain / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / Proteasome subunit alpha 1 / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / HEAT repeats / : / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / von Willebrand factor (vWF) type A domain / VWFA domain profile. / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / von Willebrand factor, type A / AAA ATPase, AAA+ lid domain / AAA+ lid domain / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / MPN domain / MPN domain profile. / Nucleophile aminohydrolases, N-terminal / von Willebrand factor A-like domain superfamily / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / 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 non-ATPase regulatory subunit 3 / 26S proteasome regulatory subunit 6A / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / 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 non-ATPase regulatory subunit 3 / 26S proteasome regulatory subunit 6A / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-4 / Proteasome subunit alpha type-5 / 26S proteasome regulatory subunit 7 / 26S proteasome regulatory subunit 6B / 26S proteasome non-ATPase regulatory subunit 8 / 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 / 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: 3.4 Å
AuthorsHsu, S.T.D. / Draczkowski, P. / Wang, Y.S.
Funding support Taiwan, 4items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)AS-CDA-109- L08 Taiwan
Ministry of Science and Technology (MoST, Taiwan)MOST 109-3114-Y-001-001 Taiwan
Ministry of Science and Technology (MoST, Taiwan)MOST 110-2113-M-001- 050-MY3 Taiwan
Ministry of Science and Technology (MoST, Taiwan)MOST 110-2311-B-001-013-MY3 Taiwan
CitationJournal: To Be Published
Title: Cryo-EM structure of human 26S proteasomal RP subcomplex bound with branched Ub chain.
Authors: Draczkowski, P. / Hsu, S.T.D. / Wang, Y.S.
History
DepositionJun 16, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 26S protease regulatory subunit 7
B: 26S protease regulatory subunit 4
C: 26S protease regulatory subunit 8
D: 26S protease regulatory subunit 6B
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
U: 26S proteasome non-ATPase regulatory subunit 1
c: 26S proteasome non-ATPase regulatory subunit 14
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
d: 26S proteasome non-ATPase regulatory subunit 8
e: 26S proteasome complex subunit DSS1
f: 26S proteasome non-ATPase regulatory subunit 2
E: 26S protease regulatory subunit 10B
F: 26S protease regulatory subunit 6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,099,78336
Polymers1,096,77825
Non-polymers3,00511
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry, native gel electrophoresis, electron microscopy, negative stain TEM, cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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26S protease regulatory subunit ... , 6 types, 6 molecules ABCDEF

#1: Protein 26S protease 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 / Cell line (production host): HEK293 / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: P35998
#2: Protein 26S protease 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMC1 / Cell line (production host): HEK293 / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: P62191
#3: Protein 26S protease 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMC5, SUG1 / Cell line (production host): HEK293 / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: P62195
#4: Protein 26S protease 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 / Cell line (production host): HEK293 / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: P43686
#24: Protein 26S protease 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMC6, SUG2 / Cell line (production host): HEK293 / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: P62333
#25: Protein 26S protease 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 / Cell line (production host): HEK293 / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: P17980

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Proteasome subunit alpha type- ... , 7 types, 7 molecules GHIJKLM

#5: 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: 27432.459 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA6, PROS27 / Cell line (production host): HEK293 / Organ (production host): Kidney / Production host: Homo sapiens (human)
References: UniProt: P60900, proteasome endopeptidase complex
#6: Protein Proteasome subunit alpha type-2 / Macropain subunit C3 / Multicatalytic endopeptidase complex subunit C3 / Proteasome component C3


Mass: 25927.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA2, HC3, PSC3 / Cell line (production host): HEK293 / Organ (production host): Kidney / Production host: Homo sapiens (human)
References: UniProt: P25787, proteasome endopeptidase complex
#7: 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: 29525.842 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA4, HC9, PSC9 / Cell line (production host): HEK293 / Organ (production host): Kidney / Production host: Homo sapiens (human)
References: UniProt: P25789, proteasome endopeptidase complex
#8: Protein Proteasome subunit alpha type-7 / Proteasome subunit RC6-1 / Proteasome subunit XAPC7


Mass: 27929.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA7, HSPC / Cell line (production host): HEK293 / Organ (production host): Kidney / Production host: Homo sapiens (human)
References: UniProt: O14818, proteasome endopeptidase complex
#9: Protein Proteasome subunit alpha type-5 / Macropain zeta chain / Multicatalytic endopeptidase complex zeta chain / Proteasome zeta chain


Mass: 26435.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA5 / Cell line (production host): HEK293 / Organ (production host): Kidney / Production host: Homo sapiens (human)
References: UniProt: P28066, proteasome endopeptidase complex
#10: 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: 29595.627 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA1, HC2, NU, PROS30, PSC2 / Cell line (production host): HEK293 / Organ (production host): Kidney / Production host: Homo sapiens (human)
References: UniProt: P25786, proteasome endopeptidase complex
#11: Protein Proteasome subunit alpha type-3 / Macropain subunit C8 / Multicatalytic endopeptidase complex subunit C8 / Proteasome component C8


Mass: 28469.252 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA3, HC8, PSC8 / Cell line (production host): HEK293 / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: P25788

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

#12: 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 / Cell line (production host): HEK293 / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: Q99460
#13: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD14, POH1 / Cell line (production host): HEK293 / Organ (production host): Kidney / Production host: Homo sapiens (human)
References: UniProt: O00487, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases
#14: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD3 / Cell line (production host): HEK293 / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: O43242
#15: 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 / Cell line (production host): HEK293 / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: O00232
#16: 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 / Cell line (production host): HEK293 / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: O00231
#17: 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 / Cell line (production host): HEK293 / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: Q15008
#18: 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 / Cell line (production host): HEK293 / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: P51665
#19: 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 / Cell line (production host): HEK293 / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: Q9UNM6
#20: 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 / Cell line (production host): HEK293 / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: P55036
#21: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD8 / Cell line (production host): HEK293 / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: P48556
#23: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD2, TRAP2 / Cell line (production host): HEK293 / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: Q13200

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Protein , 1 types, 1 molecules e

#22: Protein 26S proteasome complex subunit DSS1 / Deleted in split hand/split foot protein 1 / Split hand/foot deleted protein 1 / Split hand/foot ...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: SHFM1, DSS1, SHFDG1 / Cell line (production host): HEK293 / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: P60896

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Non-polymers , 3 types, 11 molecules

#26: 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
#27: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#28: 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

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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

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Human 26S proteasomeCOMPLEXThe images of double-capped (RP-CP-RP) 26S proteasome particles were divided into two. By merging them with a subset of single-capped (RP-CP) complexes, the signal in the particle images was partly removed, leaving only the signal of a single 19S RP and adjacent alpha subunits of the 20S CP proteasomal subcomplex.#1-#250RECOMBINANT
219S regulatory particle (RP) of human 26S proteasome.COMPLEX#1-#4, #12-#251RECOMBINANT
3AAA+-ATPase of 19S regulatory particle (RP) of human 26S proteasome.COMPLEX#1-#4, #24-#252RECOMBINANT
4Alpha subunits belonging to the 20S core particle (CP) of human 26S proteasome.COMPLEX#5-#111RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
112.5 MDaNO
21NO
31NO
41NO
54
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Homo sapiens (human)9606
54Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
21Homo sapiens (human)9606HEK-293
32Homo sapiens (human)9606HEK-293
43Homo sapiens (human)9606HEK-293
54Homo sapiens (human)9606HEK-293
Buffer solutionpH: 7.6
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
240 mMsodium chlorideNaCl1
35 mMmagnesium chlorideMgCl21
42 mM2-MercaptoethanolC2H6OS1
50.5 mM1,10-PhenanthrolineC12H8N21
62 mMadenosine triphosphateC10H16N5O13P31
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The complex was additionally supplemented with an excess of preformed and SEC-purified human RPN13:UCHL5 complex.
Specimen supportDetails: 20 mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: incubation time= 3 s blotting time= 2.5 s

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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 FIELD / Nominal magnification: 70000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.8 sec. / Electron dose: 49 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 3 / Num. of real images: 15242
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategoryDetails
1Topazparticle selection
2EPUimage acquisitiondata collection
3RELION3.1image acquisitiondata processing
4cryoSPARC3.1image acquisitiondata processing
6CTFFIND4.1CTF correction
9UCSF ChimeraX1.3model fitting
11PHENIX1.19.2model refinement
12Coot0.9.4.1 ELmodel refinement
13RELION3.1initial Euler assignment
14cryoSPARC3.1final Euler assignmentNon-uniform Refinment
15RELION3.1classification
16cryoSPARC3.13D reconstructionNon-uniform Refinment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2695911
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 153646 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 88 / Protocol: OTHER / Space: REAL / Target criteria: 0.8
Atomic model buildingPDB-ID: 6MSB

6msb


Accession code: 6MSB / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 88.35 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00363536
ELECTRON MICROSCOPYf_angle_d0.60386341
ELECTRON MICROSCOPYf_dihedral_angle_d13.91422050
ELECTRON MICROSCOPYf_chiral_restr0.04310216
ELECTRON MICROSCOPYf_plane_restr0.00411375

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