[English] 日本語
Yorodumi
- PDB-6epe: Substrate processing state 26S proteasome (SPS2) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6epe
TitleSubstrate processing state 26S proteasome (SPS2)
Components
  • (26S proteasome non-ATPase regulatory subunit ...) x 4
  • (26S proteasome regulatory subunit ...) x 5
  • (Proteasome (Prosome, macropain) 26S subunit, non-ATPase, ...) x 5
  • (Proteasome 26S subunit, ...) x 2
  • (Proteasome subunit alpha type- ...) x 7
  • (Proteasome subunit beta type- ...) x 7
  • 26S proteasome subunit S5aProteasome
  • RCG28037
KeywordsHYDROLASE / UPS / Substrate processing state / Neuron degeneration
Function / homology
Function and homology information


fluid transport / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / meiosis I / modulation by host of viral transcription / thyrotropin-releasing hormone receptor binding / positive regulation of inclusion body assembly / negative regulation of inflammatory response to antigenic stimulus / proteasome accessory complex / regulation of endopeptidase activity / proteasome-activating ATPase activity ...fluid transport / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / meiosis I / modulation by host of viral transcription / thyrotropin-releasing hormone receptor binding / positive regulation of inclusion body assembly / negative regulation of inflammatory response to antigenic stimulus / proteasome accessory complex / regulation of endopeptidase activity / proteasome-activating ATPase activity / proteasome regulatory particle / nuclear proteasome complex / proteasome regulatory particle, lid subcomplex / immune system process / proteasome regulatory particle, base subcomplex / protein K63-linked deubiquitination / blastocyst development / Lys63-specific deubiquitinase activity / cytosolic proteasome complex / myofibril / proteasome binding / enzyme regulator activity / polyubiquitin modification-dependent protein binding / regulation of protein catabolic process / NF-kappaB binding / endopeptidase activator activity / proteasomal ubiquitin-independent protein catabolic process / proteasome storage granule / proteasome complex / polysome / proteasome core complex / inclusion body / proteasome core complex, beta-subunit complex / stem cell differentiation / thiol-dependent ubiquitin-specific protease activity / proteasome endopeptidase complex / proteasome core complex, alpha-subunit complex / ubiquitin-dependent ERAD pathway / proteasome assembly / thiol-dependent ubiquitinyl hydrolase activity / threonine-type endopeptidase activity / mRNA export from nucleus / response to organonitrogen compound / sarcomere / TBP-class protein binding / regulation of proteasomal protein catabolic process / proteolysis involved in cellular protein catabolic process / proteasomal protein catabolic process / metallopeptidase activity / positive regulation of RNA polymerase II transcriptional preinitiation complex assembly / P-body / response to virus / protein catabolic process / negative regulation of neuron death / lipopolysaccharide binding / double-strand break repair via homologous recombination / response to organic cyclic compound / nuclear matrix / postsynapse / modulation of chemical synaptic transmission / proteasome-mediated ubiquitin-dependent protein catabolic process / double-strand break repair via nonhomologous end joining / cytoplasmic vesicle / peptidase activity / ubiquitin-dependent protein catabolic process / hydrolase activity / response to oxidative stress / endopeptidase activity / response to ethanol / dendritic spine / positive regulation of NF-kappaB transcription factor activity / ATPase activity / protein deubiquitination / centrosome / synapse / regulation of transcription by RNA polymerase II / signaling receptor binding / transcription factor binding / proteolysis / negative regulation of transcription, DNA-templated / ubiquitin protein ligase binding / structural molecule activity / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / RNA binding / membrane / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / Proteasome subunit alpha6 / Rpn11/EIF3F, C-terminal / P-loop containing nucleoside triphosphate hydrolase / Nucleophile aminohydrolases, N-terminal / Proteasomal ATPase OB C-terminal domain / CSN8/PSMD8/EIF3K / Proteasome beta 3 subunit / Proteasome subunit alpha5 / 26S Proteasome non-ATPase regulatory subunit 7/8 ...26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / Proteasome subunit alpha6 / Rpn11/EIF3F, C-terminal / P-loop containing nucleoside triphosphate hydrolase / Nucleophile aminohydrolases, N-terminal / Proteasomal ATPase OB C-terminal domain / CSN8/PSMD8/EIF3K / Proteasome beta 3 subunit / Proteasome subunit alpha5 / 26S Proteasome non-ATPase regulatory subunit 7/8 / Proteasome subunit alpha2 / Proteasome B-type subunit / Proteasome subunit beta 6 / Proteasome subunit alpha 1 / Proteasome subunit alpha 7 / Proteasome subunit beta 1 / Proteasome subunit beta 2 / Proteasome subunit beta 7 / 26S Proteasome regulatory subunit 4 / 26S Proteasome regulatory subunit 7 / Proteasome beta subunit, C-terminal / Proteasome alpha-type subunit / 26S proteasome regulatory subunit 10B / ATPase, AAA-type, conserved site / JAB1/MPN/MOV34 metalloenzyme domain / Proteasome component (PCI) domain / Proteasome, subunit alpha/beta / Proteasome/cyclosome repeat / von Willebrand factor, type A / AAA+ ATPase domain / Ubiquitin interacting motif / ATPase, AAA-type, core / 26S proteasome regulatory subunit P45-like / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 26S proteasome non-ATPase regulatory subunit Rpn12 / DSS1/SEM1 / Armadillo-like helical / 26S proteasome regulatory subunit, C-terminal / Armadillo-type fold / Proteasome beta-type subunit, conserved site / Proteasome subunit beta 4 / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / 26S Proteasome regulatory subunit 6B / 26S Proteasome non-ATPase regulatory subunit 1 / Peptidase T1A, proteasome beta-subunit / 26S proteasome regulatory subunit RPN6 N-terminal domain / AAA+ lid domain / Proteasomal ATPase OB C-terminal domain / Proteasome/cyclosome repeat / HEAT repeats / RPN1/RPN2 N-terminal domain / 26S proteasome regulatory subunit RPN2 C-terminal domain / PCI domain / 26S proteasome regulatory subunit RPN5 C-terminal domain / 26S proteasome subunit RPN6 C-terminal helix domain / Proteasome subunit A N-terminal signature / 26S proteasome subunit RPN7 / Proteasome regulatory subunit C-terminal / CSN8/PSMD8/EIF3K family / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Maintenance of mitochondrial structure and function / Ubiquitin interaction motif / von Willebrand factor type A domain / DSS1/SEM1 family / ATPase family associated with various cellular activities (AAA) / Proteasome beta subunits C terminal / 26S proteasome non-ATPase regulatory subunit 3 / MPN domain / 26S Proteasome non-ATPase regulatory subunit 6 / 26S Proteasome non-ATPase regulatory subunit 11 / 26S Proteasome non-ATPase regulatory subunit 12 / 26S Proteasome non-ATPase regulatory subunit 13 / 26S Proteasome non-ATPase regulatory subunit 14 / Winged helix-like DNA-binding domain superfamily / Winged helix DNA-binding domain superfamily / von Willebrand factor A-like domain superfamily / Proteasome subunit alpha 3 / Proteasome subunit / Proteasome subunit beta 5 / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / 26S proteasome regulatory subunit RPN2, C-terminal / 26S proteasome regulatory subunit Rpn6, N-terminal / 6S proteasome subunit Rpn6, C-terminal helix domain / RPN1/RPN2, N-terminal / 26S proteasome regulatory subunit RPN5, C-terminal domain / 26S proteasome non-ATPase regulatory subunit RPN1, C-terminal / AAA ATPase, AAA+ lid domain / Proteasome alpha-subunit, N-terminal domain / Tetratricopeptide-like helical domain superfamily
Proteasome subunit beta type-2 / Proteasome subunit alpha type-4 / Proteasome subunit alpha type-3 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / 26S proteasome non-ATPase regulatory subunit 1 / Proteasome 26S subunit, ATPase 6 / 26S proteasome non-ATPase regulatory subunit 11 / Proteasome 26S subunit, non-ATPase 8 ...Proteasome subunit beta type-2 / Proteasome subunit alpha type-4 / Proteasome subunit alpha type-3 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / 26S proteasome non-ATPase regulatory subunit 1 / Proteasome 26S subunit, ATPase 6 / 26S proteasome non-ATPase regulatory subunit 11 / Proteasome 26S subunit, non-ATPase 8 / Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 7 (Predicted) / RCG28037 / 26S proteasome non-ATPase regulatory subunit 13 / Proteasome subunit beta type-6 / Proteasome subunit beta type-5 / Proteasome subunit alpha type-7 / Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 12 / Proteasome subunit alpha type-6 / 26S proteasome regulatory subunit 4 / 26S proteasome regulatory subunit 8 / Proteasome subunit beta type-3 / Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 14 / Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 3 / 26S proteasome regulatory subunit 7 / Proteasome subunit alpha type-5 / 26S proteasome regulatory subunit 6A / 26S proteasome regulatory subunit 6B / 26S proteasome regulatory subunit 6A / Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 6 / 26S proteasome subunit S5a / Proteasome subunit beta type-7 / Proteasome subunit beta type-4 / 26S proteasome non-ATPase regulatory subunit 2
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 12.8 Å
AuthorsGuo, Q. / Lehmer, C. / Martinez-Sanchez, A. / Rudack, T. / Beck, F. / Hartmann, H. / Hipp, M.S. / Hartl, F.U. / Edbauer, D. / Baumeister, W. / Fernandez-Busnadiego, R.
Funding support Germany, United States, 4items
OrganizationGrant numberCountry
European CommissionFP7 GA ERC-2012-SyG_318987-ToPAG Germany
European CommissionFP7 GA ERC-2013-CoG_617198 DPR-MODELS Germany
German Research FoundationSFB-1035/Project A01 Germany
National Institutes of Health9P41GM104601 United States
CitationJournal: Cell / Year: 2018
Title: In Situ Structure of Neuronal C9orf72 Poly-GA Aggregates Reveals Proteasome Recruitment.
Authors: Qiang Guo / Carina Lehmer / Antonio Martínez-Sánchez / Till Rudack / Florian Beck / Hannelore Hartmann / Manuela Pérez-Berlanga / Frédéric Frottin / Mark S Hipp / F Ulrich Hartl / ...Authors: Qiang Guo / Carina Lehmer / Antonio Martínez-Sánchez / Till Rudack / Florian Beck / Hannelore Hartmann / Manuela Pérez-Berlanga / Frédéric Frottin / Mark S Hipp / F Ulrich Hartl / Dieter Edbauer / Wolfgang Baumeister / Rubén Fernández-Busnadiego /
Abstract: Protein aggregation and dysfunction of the ubiquitin-proteasome system are hallmarks of many neurodegenerative diseases. Here, we address the elusive link between these phenomena by employing cryo- ...Protein aggregation and dysfunction of the ubiquitin-proteasome system are hallmarks of many neurodegenerative diseases. Here, we address the elusive link between these phenomena by employing cryo-electron tomography to dissect the molecular architecture of protein aggregates within intact neurons at high resolution. We focus on the poly-Gly-Ala (poly-GA) aggregates resulting from aberrant translation of an expanded GGGGCC repeat in C9orf72, the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia. We find that poly-GA aggregates consist of densely packed twisted ribbons that recruit numerous 26S proteasome complexes, while other macromolecules are largely excluded. Proximity to poly-GA ribbons stabilizes a transient substrate-processing conformation of the 26S proteasome, suggesting stalled degradation. Thus, poly-GA aggregates may compromise neuronal proteostasis by driving the accumulation and functional impairment of a large fraction of cellular proteasomes.
Validation Report
SummaryFull reportAbout validation report
History
DepositionOct 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 11, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-3915
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proteasome subunit alpha type-6
B: Proteasome subunit alpha type-2
C: Proteasome subunit alpha type-4
D: Proteasome subunit alpha type-7
E: Proteasome subunit alpha type-5
F: Proteasome subunit alpha type-1
G: Proteasome subunit alpha type-3
1: Proteasome subunit beta type-6
2: Proteasome subunit beta type-7
3: Proteasome subunit beta type-3
4: Proteasome subunit beta type-2
5: Proteasome subunit beta type-5
6: Proteasome subunit beta type-1
7: Proteasome subunit beta type-4
W: 26S proteasome subunit S5a
V: Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 14
T: Proteasome 26S subunit, non-ATPase 8
Y: RCG28037
Z: 26S proteasome non-ATPase regulatory subunit 2
N: 26S proteasome non-ATPase regulatory subunit 1
S: Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 3
P: Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 12
Q: 26S proteasome non-ATPase regulatory subunit 11
R: Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 6
U: Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 7 (Predicted)
O: 26S proteasome non-ATPase regulatory subunit 13
H: 26S proteasome regulatory subunit 7
I: 26S proteasome regulatory subunit 4
K: 26S proteasome regulatory subunit 6B
L: Proteasome 26S subunit, ATPase 6
M: 26S proteasome regulatory subunit 6A
J: 26S proteasome regulatory subunit 8


Theoretical massNumber of molelcules
Total (without water)1,284,00332
Polymers1,284,00332
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area218600 Å2
ΔGint-887 kcal/mol
Surface area316700 Å2
MethodPISA

-
Components

+
Proteasome subunit alpha type- ... , 7 types, 7 molecules ABCDEFG

#1: Protein Proteasome subunit alpha type-6 / / Macropain iota chain / Multicatalytic endopeptidase complex iota chain / Proteasome iota chain


Mass: 27432.459 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat)
References: UniProt: P60901, proteasome endopeptidase complex
#2: Protein Proteasome subunit alpha type-2 / / Macropain subunit C3 / Multicatalytic endopeptidase complex subunit C3 / Proteasome component C3


Mass: 25955.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat)
References: UniProt: P17220, proteasome endopeptidase complex
#3: 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: 29539.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat)
References: UniProt: P21670, proteasome endopeptidase complex
#4: Protein Proteasome subunit alpha type-7 / / Proteasome subunit RC6-1


Mass: 28369.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat)
References: UniProt: P48004, proteasome endopeptidase complex
#5: Protein Proteasome subunit alpha type-5 / / Macropain zeta chain / Multicatalytic endopeptidase complex zeta chain / Proteasome zeta chain


Mass: 26416.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat)
References: UniProt: P34064, proteasome endopeptidase complex
#6: Protein Proteasome subunit alpha type-1 / / Macropain subunit C2 / Multicatalytic endopeptidase complex subunit C2 / Proteasome component C2 / ...Macropain subunit C2 / Multicatalytic endopeptidase complex subunit C2 / Proteasome component C2 / Proteasome nu chain


Mass: 29557.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat)
References: UniProt: P18420, proteasome endopeptidase complex
#7: 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 K


Mass: 28456.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat)
References: UniProt: P18422, proteasome endopeptidase complex

+
Proteasome subunit beta type- ... , 7 types, 7 molecules 1234567

#8: Protein Proteasome subunit beta type-6 / / Macropain delta chain / Multicatalytic endopeptidase complex delta chain / Proteasome chain 5 / ...Macropain delta chain / Multicatalytic endopeptidase complex delta chain / Proteasome chain 5 / Proteasome delta chain / Proteasome subunit Y


Mass: 25309.576 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat)
References: UniProt: P28073, proteasome endopeptidase complex
#9: Protein Proteasome subunit beta type-7 / / Macropain chain Z / Multicatalytic endopeptidase complex chain Z / Proteasome subunit Z


Mass: 29963.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat)
References: UniProt: Q9JHW0, proteasome endopeptidase complex
#10: Protein Proteasome subunit beta type-3 / PSMB3 / Proteasome chain 13 / Proteasome component C10-II / Proteasome theta chain


Mass: 22988.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat)
References: UniProt: P40112, proteasome endopeptidase complex
#11: Protein Proteasome subunit beta type-2 / PSMB2 / Macropain subunit C7-I / Multicatalytic endopeptidase complex subunit C7-I / Proteasome component C7-I


Mass: 22941.381 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat)
References: UniProt: P40307, proteasome endopeptidase complex
#12: 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 X


Mass: 28615.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat)
References: UniProt: P28075, proteasome endopeptidase complex
#13: 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: 26511.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat)
References: UniProt: P18421, proteasome endopeptidase complex
#14: Protein Proteasome subunit beta type-4 / PSMB4 / Macropain beta chain / Multicatalytic endopeptidase complex beta chain / Proteasome beta chain / ...Macropain beta chain / Multicatalytic endopeptidase complex beta chain / Proteasome beta chain / Proteasome chain 3 / RN3


Mass: 29226.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat)
References: UniProt: P34067, proteasome endopeptidase complex

+
Protein , 2 types, 2 molecules WY

#15: Protein 26S proteasome subunit S5a / Proteasome / Psmd4 protein


Mass: 40775.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q9ESH1
#18: Protein RCG28037 / SEM1 / 26S proteasome complex subunit


Mass: 8284.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: D3ZHW9

+
Proteasome (Prosome, macropain) 26S subunit, non-ATPase, ... , 5 types, 5 molecules VSPRU

#16: Protein Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 14 / Proteasome 26S subunit / non-ATPase 14 / Psmd14 protein / RCG26455 / isoform CRA_b


Mass: 34620.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q4V8E2
#21: Protein Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 3 / Proteasome (Prosome / macropain) 26S subunit / non-ATPase / 3 / isoform CRA_b / Proteasome 26S ...Proteasome (Prosome / macropain) 26S subunit / non-ATPase / 3 / isoform CRA_b / Proteasome 26S subunit / non-ATPase 3


Mass: 60778.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q5U2S7
#22: Protein Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 12 / Proteasome 26S subunit / non-ATPase 12


Mass: 53011.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q5XIC6
#24: Protein Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 6 / Proteasome (Prosome / macropain) 26S subunit / non-ATPase / 6 / isoform CRA_a / Proteasome 26S ...Proteasome (Prosome / macropain) 26S subunit / non-ATPase / 6 / isoform CRA_a / Proteasome 26S subunit / non-ATPase 6


Mass: 45658.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q6PCT9
#25: Protein Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 7 (Predicted) / Proteasome 26S subunit / non-ATPase 7


Mass: 36551.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: D4AEH3

+
Proteasome 26S subunit, ... , 2 types, 2 molecules TL

#17: Protein Proteasome 26S subunit, non-ATPase 8


Mass: 39932.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: F1LMQ3
#30: Protein Proteasome 26S subunit, ATPase 6 / RCG61291


Mass: 45867.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: G3V6W6

+
26S proteasome non-ATPase regulatory subunit ... , 4 types, 4 molecules ZNQO

#19: Protein 26S proteasome non-ATPase regulatory subunit 2


Mass: 100300.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q4FZT9
#20: Protein 26S proteasome non-ATPase regulatory subunit 1 / 26S proteasome regulatory subunit RPN2 / 26S proteasome regulatory subunit S1 / 26S proteasome subunit p112


Mass: 105870.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: O88761
#23: Protein 26S proteasome non-ATPase regulatory subunit 11 / 26S proteasome regulatory subunit RPN6


Mass: 47526.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: F1LMZ8
#26: 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: 42867.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: B0BN93

+
26S proteasome regulatory subunit ... , 5 types, 5 molecules HIKMJ

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


Mass: 48640.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q63347
#28: 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) Rattus norvegicus (Norway rat) / References: UniProt: P62193
#29: Protein 26S proteasome regulatory subunit 6B / 26S proteasome AAA-ATPase subunit RPT3 / Proteasome 26S subunit ATPase 4 / S6 ATPase / Tat-binding ...26S proteasome AAA-ATPase subunit RPT3 / Proteasome 26S subunit ATPase 4 / S6 ATPase / Tat-binding protein 7 / TBP-7


Mass: 47468.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q63570
#31: Protein 26S proteasome regulatory subunit 6A / Proteasome (Prosome / macropain) 26S subunit / ATPase 3 / isoform CRA_a


Mass: 49611.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q6P6U2, UniProt: Q63569*PLUS
#32: Protein 26S proteasome regulatory subunit 8 / 26S proteasome AAA-ATPase subunit RPT6 / Proteasome 26S subunit ATPase 5 / Proteasome subunit p45 / ...26S proteasome AAA-ATPase subunit RPT6 / Proteasome 26S subunit ATPase 5 / Proteasome subunit p45 / Thyroid hormone receptor-interacting protein 1 / TRIP1 / p45/SUG


Mass: 45694.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P62198

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: subtomogram averaging

-
Sample preparation

ComponentName: Substrate processing state 26S proteasome (SPS2) / Type: COMPLEX
Details: in situ proteasome structure generated by subtomogram averaging
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32
Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Buffer solutionpH: 7
SpecimenDetails: FIB milled rat primary neurons / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: The grid was coated with C prior to use / Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 298 K

-
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 / Nominal magnification: 42000 X / Nominal defocus max: 7000 nm / Nominal defocus min: 5000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.4 sec. / Electron dose: 1.8 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansWidth: 3838 / Height: 3710

-
Processing

EM software
IDNameVersionCategory
1PyTomvolume selection
2TOM Toolboxvolume selection
3RELION1.4volume selection
4SerialEMimage acquisition
6CTFFINDCTF correction
7RELION1.4CTF correction
10MDFFmodel fitting
14RELION1.4final Euler assignment
15RELION1.4classification
16RELION1.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 12.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3482 / Symmetry type: POINT
EM volume selectionMethod: Template matching / Num. of tomograms: 9 / Num. of volumes extracted: 10367 / Reference model: average of manual picked subtomograms
Atomic model buildingProtocol: FLEXIBLE FIT

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB at PDBe / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.:Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.:Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more