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Entry
Database: PDB / ID: 4cr4
TitleDeep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome
Components
  • (26S PROTEASE REGULATORY SUBUNIT ...) x 5
  • (26S PROTEASOME REGULATORY SUBUNIT ...) x 12
  • (PROTEASOME COMPONENT ...) x 14
  • 26S PROTEASE SUBUNIT RPT4
  • 26S PROTEASOME COMPLEX SUBUNIT SEM1
KeywordsHYDROLASE / AAA-ATPASE / ATP-ANALOG / CLASSIFICATION
Function / homology
Function and homology information


SAGA complex localization to transcription regulatory region / Metalloprotease DUBs / peroxisome fission / proteasome storage granule assembly / transcription export complex 2 / proteasome regulatory particle assembly / protein deneddylation / maintenance of DNA trinucleotide repeats / filamentous growth / COP9 signalosome ...SAGA complex localization to transcription regulatory region / Metalloprotease DUBs / peroxisome fission / proteasome storage granule assembly / transcription export complex 2 / proteasome regulatory particle assembly / protein deneddylation / maintenance of DNA trinucleotide repeats / filamentous growth / COP9 signalosome / proteasome regulatory particle / cytosolic proteasome complex / proteasome regulatory particle, lid subcomplex / protein-containing complex localization / proteasome-activating activity / mitochondrial fission / proteasome regulatory particle, base subcomplex / metal-dependent deubiquitinase activity / nonfunctional rRNA decay / K48-linked polyubiquitin modification-dependent protein binding / proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / peptide catabolic process / CDK-mediated phosphorylation and removal of Cdc6 / proteasome binding / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / Neddylation / regulation of protein catabolic process / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / endopeptidase activator activity / polyubiquitin modification-dependent protein binding / proteasome assembly / positive regulation of RNA polymerase II transcription preinitiation complex assembly / protein deubiquitination / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / Ub-specific processing proteases / threonine-type endopeptidase activity / mRNA export from nucleus / enzyme regulator activity / ERAD pathway / protein folding chaperone / Neutrophil degranulation / proteasome complex / ubiquitin binding / nucleotide-excision repair / positive regulation of transcription elongation by RNA polymerase II / double-strand break repair via homologous recombination / positive regulation of protein catabolic process / metallopeptidase activity / peroxisome / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / molecular adaptor activity / regulation of cell cycle / chromatin remodeling / protein domain specific binding / mRNA binding / ubiquitin protein ligase binding / endoplasmic reticulum membrane / structural molecule activity / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Rpn9, C-terminal helix / Rpn9 C-terminal helix / Proteasomal ubiquitin receptor Rpn13/ADRM1 / Proteasomal ubiquitin receptor Rpn13/ADRM1, Pru domain superfamily / Rpn13/ADRM1, Pru domain / Proteasome complex subunit Rpn13, Pru domain / Pru (pleckstrin-like receptor for ubiquitin) domain profile. / : / 26S proteasome regulatory subunit RPN7/PSMD6 C-terminal helix / 26S proteasome non-ATPase regulatory subunit Rpn12 ...Rpn9, C-terminal helix / Rpn9 C-terminal helix / Proteasomal ubiquitin receptor Rpn13/ADRM1 / Proteasomal ubiquitin receptor Rpn13/ADRM1, Pru domain superfamily / Rpn13/ADRM1, Pru domain / Proteasome complex subunit Rpn13, Pru domain / Pru (pleckstrin-like receptor for ubiquitin) domain profile. / : / 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 / DSS1/SEM1 / 26S proteasome regulatory subunit RPN5, C-terminal domain / : / DSS1/SEM1 family / 26S proteasome regulatory subunit RPN5 C-terminal domain / PSD13 N-terminal repeats / DSS1_SEM1 / 26S proteasome regulatory subunit Rpn6, N-terminal / 6S proteasome subunit Rpn6, C-terminal helix domain / 26S proteasome regulatory subunit RPN6 N-terminal domain / 26S proteasome subunit RPN6 C-terminal helix domain / 26S Proteasome non-ATPase regulatory subunit 13 / : / 26S proteasome subunit RPN2, N-terminal domain / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / 26S proteasome regulatory subunit RPN2, C-terminal / 26S proteasome regulatory subunit RPN2 C-terminal domain / 26S Proteasome non-ATPase regulatory subunit 7/8 / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / RPN1, N-terminal / 26S proteasome non-ATPase regulatory subunit RPN1, C-terminal / : / RPN1 N-terminal domain / 26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / 26S proteasome regulatory subunit 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 / PCI/PINT associated module / : / von Willebrand factor type A domain / HEAT repeats / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / : / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / VWFA domain profile. / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / von Willebrand factor, type A / AAA ATPase, AAA+ lid domain / AAA+ lid domain / TPR repeat region circular profile. / ATPase, AAA-type, conserved site / AAA-protein family signature. / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / TPR repeat profile. / MPN domain / MPN domain profile. / Nucleophile aminohydrolases, N-terminal / von Willebrand factor A-like domain superfamily / Tetratricopeptide repeat
Similarity search - Domain/homology
26S proteasome regulatory subunit RPN13 / 26S proteasome complex subunit SEM1 / Probable proteasome subunit alpha type-7 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-6 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 ...26S proteasome regulatory subunit RPN13 / 26S proteasome complex subunit SEM1 / Probable proteasome subunit alpha type-7 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-6 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 / Proteasome subunit beta type-5 / Proteasome subunit beta type-7 / Proteasome subunit alpha type-5 / 26S proteasome regulatory subunit RPN12 / 26S proteasome regulatory subunit RPN2 / 26S proteasome regulatory subunit 6A / 26S proteasome regulatory subunit 6B homolog / 26S proteasome regulatory subunit 7 homolog / Proteasome subunit beta type-1 / 26S proteasome regulatory subunit RPN1 / 26S proteasome regulatory subunit RPN10 / 26S proteasome regulatory subunit RPN3 / Proteasome subunit alpha type-6 / Proteasome subunit alpha type-4 / 26S proteasome regulatory subunit 4 homolog / Ubiquitin carboxyl-terminal hydrolase RPN11 / 26S proteasome subunit RPT4 / 26S proteasome regulatory subunit 8 homolog / 26S proteasome regulatory subunit RPN9 / 26S proteasome regulatory subunit RPN7 / 26S proteasome regulatory subunit RPN8 / 26S proteasome regulatory subunit RPN5 / 26S proteasome regulatory subunit RPN6
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.8 Å
AuthorsUnverdorben, P. / Beck, F. / Sledz, P. / Schweitzer, A. / Pfeifer, G. / Plitzko, J.M. / Baumeister, W. / Foerster, F.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2014
Title: Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome.
Authors: Pia Unverdorben / Florian Beck / Paweł Śledź / Andreas Schweitzer / Günter Pfeifer / Jürgen M Plitzko / Wolfgang Baumeister / Friedrich Förster /
Abstract: The 26S proteasome is a 2.5 MDa molecular machine that executes the degradation of substrates of the ubiquitin-proteasome pathway. The molecular architecture of the 26S proteasome was recently ...The 26S proteasome is a 2.5 MDa molecular machine that executes the degradation of substrates of the ubiquitin-proteasome pathway. The molecular architecture of the 26S proteasome was recently established by cryo-EM approaches. For a detailed understanding of the sequence of events from the initial binding of polyubiquitylated substrates to the translocation into the proteolytic core complex, it is necessary to move beyond static structures and characterize the conformational landscape of the 26S proteasome. To this end we have subjected a large cryo-EM dataset acquired in the presence of ATP and ATP-γS to a deep classification procedure, which deconvolutes coexisting conformational states. Highly variable regions, such as the density assigned to the largest subunit, Rpn1, are now well resolved and rendered interpretable. Our analysis reveals the existence of three major conformations: in addition to the previously described ATP-hydrolyzing (ATPh) and ATP-γS conformations, an intermediate state has been found. Its AAA-ATPase module adopts essentially the same topology that is observed in the ATPh conformation, whereas the lid is more similar to the ATP-γS bound state. Based on the conformational ensemble of the 26S proteasome in solution, we propose a mechanistic model for substrate recognition, commitment, deubiquitylation, and translocation into the core particle.
History
DepositionFeb 25, 2014Deposition site: PDBE / Processing site: PDBE
SupersessionApr 2, 2014ID: 4C0V
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2Apr 30, 2014Group: Database references
Revision 1.3Aug 30, 2017Group: Data collection / Category: em_image_scans
Revision 1.4Oct 3, 2018Group: Data collection
Category: diffrn_radiation / diffrn_radiation_wavelength / em_software
Item: _em_software.image_processing_id / _em_software.name
Revision 1.5May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. ... SHEET DETERMINATION METHOD: AUTHOR PROVIDED. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Assembly

Deposited unit
1: PROTEASOME COMPONENT PRE3
2: PROTEASOME COMPONENT PUP1
3: PROTEASOME COMPONENT PUP3
4: PROTEASOME COMPONENT C11
5: PROTEASOME COMPONENT PRE2
6: PROTEASOME COMPONENT C5
7: PROTEASOME COMPONENT PRE4
A: PROTEASOME COMPONENT C7-ALPHA
B: PROTEASOME COMPONENT Y7
C: PROTEASOME COMPONENT Y13
D: PROTEASOME COMPONENT PRE6
E: PROTEASOME COMPONENT PUP2
F: PROTEASOME COMPONENT PRE5
G: PROTEASOME COMPONENT C1
H: 26S PROTEASE REGULATORY SUBUNIT 7 HOMOLOG
I: 26S PROTEASE REGULATORY SUBUNIT 4 HOMOLOG
J: 26S PROTEASE REGULATORY SUBUNIT 8 HOMOLOG
K: 26S PROTEASE REGULATORY SUBUNIT 6B HOMOLOG
L: 26S PROTEASE SUBUNIT RPT4
M: 26S PROTEASE REGULATORY SUBUNIT 6A
N: 26S PROTEASOME REGULATORY SUBUNIT RPN2
O: 26S PROTEASOME REGULATORY SUBUNIT RPN9
P: 26S PROTEASOME REGULATORY SUBUNIT RPN5
Q: 26S PROTEASOME REGULATORY SUBUNIT RPN6
R: 26S PROTEASOME REGULATORY SUBUNIT RPN7
S: 26S PROTEASOME REGULATORY SUBUNIT RPN3
T: 26S PROTEASOME REGULATORY SUBUNIT RPN12
U: 26S PROTEASOME REGULATORY SUBUNIT RPN8
V: 26S PROTEASOME REGULATORY SUBUNIT RPN11
W: 26S PROTEASOME REGULATORY SUBUNIT RPN10
X: 26S PROTEASOME REGULATORY SUBUNIT RPN13
Y: 26S PROTEASOME COMPLEX SUBUNIT SEM1
Z: 26S PROTEASOME REGULATORY SUBUNIT RPN1


Theoretical massNumber of molelcules
Total (without water)1,309,28433
Polymers1,309,28433
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

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PROTEASOME COMPONENT ... , 14 types, 14 molecules 1234567ABCDEFG

#1: Protein PROTEASOME COMPONENT PRE3 / 20S PROTEASOME BETA SUBUNIT 1 / MACROPAIN SUBUNIT PRE3 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX ...20S PROTEASOME BETA SUBUNIT 1 / MACROPAIN SUBUNIT PRE3 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PRE3 / PROTEINASE YSCE SUBUNIT PRE3


Mass: 23573.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P38624, proteasome endopeptidase complex
#2: Protein PROTEASOME COMPONENT PUP1 / 20S PROTEASOME BETA SUBUNIT 2 MACROPAIN SUBUNIT PUP1 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT ...20S PROTEASOME BETA SUBUNIT 2 MACROPAIN SUBUNIT PUP1 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PUP1 / PROTEINASE YSCE SUBUNIT PUP1


Mass: 28299.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P25043, proteasome endopeptidase complex
#3: Protein PROTEASOME COMPONENT PUP3 / 20S PROTEASOME BETA SUBUNIT 3 / MACROPAIN SUBUNIT PUP3 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PUP3


Mass: 22627.842 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P25451, proteasome endopeptidase complex
#4: Protein PROTEASOME COMPONENT C11 / 20S PROTEASOME BETA SUBUNIT 4 / MACROPAIN SUBUNIT C11 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX ...20S PROTEASOME BETA SUBUNIT 4 / MACROPAIN SUBUNIT C11 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C11 / PROTEINASE YSCE SUBUNIT 11


Mass: 22545.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P22141, proteasome endopeptidase complex
#5: Protein PROTEASOME COMPONENT PRE2 / 20S PROTEASOME BETA SUBUNIT 5 / MACROPAIN SUBUNIT PRE2 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX ...20S PROTEASOME BETA SUBUNIT 5 / MACROPAIN SUBUNIT PRE2 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PRE2 / PROTEINASE YSCE SUBUNIT PRE2


Mass: 31698.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P30656, proteasome endopeptidase complex
#6: Protein PROTEASOME COMPONENT C5 / 20S PROTEASOME BETA SUBUNIT 6 / MULTICATALYTIC ENDOPEPTIDASE


Mass: 26905.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P23724, proteasome endopeptidase complex
#7: Protein PROTEASOME COMPONENT PRE4 / 20S PROTEASOME BETA SUBUNIT 7 / MACROPAIN SUBUNIT PRE4 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX ...20S PROTEASOME BETA SUBUNIT 7 / MACROPAIN SUBUNIT PRE4 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PRE4 / PROTEINASE YSCE SUBUNIT PRE4


Mass: 29471.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P30657, proteasome endopeptidase complex
#8: Protein PROTEASOME COMPONENT C7-ALPHA / 20S PROTEASOME ALPHA SUBUNIT 1 / MACROPAIN SUBUNIT C7-ALPHA / MULTICATALYTIC ENDOPEPTIDASE COMPLEX ...20S PROTEASOME ALPHA SUBUNIT 1 / MACROPAIN SUBUNIT C7-ALPHA / MULTICATALYTIC ENDOPEPTIDASE COMPLEX C7 / PROTEASOME COMPONENT Y8 / PROTEINASE YSCE SUBUNIT 7 / SCL1 SUPPRESSOR PROTEIN


Mass: 28033.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P21243, proteasome endopeptidase complex
#9: Protein PROTEASOME COMPONENT Y7 / 20S PROTEASOME ALPHA SUBUNIT 2 / MACROPAIN SUBUNIT Y7 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX ...20S PROTEASOME ALPHA SUBUNIT 2 / MACROPAIN SUBUNIT Y7 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT Y7 / PROTEINASE YSCE SUBUNIT 7


Mass: 27191.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P23639, proteasome endopeptidase complex
#10: Protein PROTEASOME COMPONENT Y13 / 20S PROTEASOME ALPHA SUBUNIT 3 / MACROPAIN SUBUNIT Y13 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX ...20S PROTEASOME ALPHA SUBUNIT 3 / MACROPAIN SUBUNIT Y13 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT Y13 / PROTEINASE YSCE SUBUNIT 13


Mass: 28748.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P23638, proteasome endopeptidase complex
#11: Protein PROTEASOME COMPONENT PRE6 / 20S PROTEASOME ALPHA SUBUNIT 4 / MACROPAIN SUBUNIT PRE6 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX ...20S PROTEASOME ALPHA SUBUNIT 4 / MACROPAIN SUBUNIT PRE6 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PRE6 / PROTEINASE YSCE SUBUNIT PRE6


Mass: 28478.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P40303, proteasome endopeptidase complex
#12: Protein PROTEASOME COMPONENT PUP2 / 20S PROTEASOME ALPHA SUBUNIT 5 / MACROPAIN SUBUNIT PUP2 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX ...20S PROTEASOME ALPHA SUBUNIT 5 / MACROPAIN SUBUNIT PUP2 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PUP2 / PROTEINASE YSCE SUBUNIT PUP2


Mass: 28649.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P32379, proteasome endopeptidase complex
#13: Protein PROTEASOME COMPONENT PRE5 / 20S PROTEASOME ALPHA SUBUNIT 6 / MACROPAIN SUBUNIT PRE5 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX ...20S PROTEASOME ALPHA SUBUNIT 6 / MACROPAIN SUBUNIT PRE5 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PRE5 / PROTEINASE YSCE SUBUNIT PRE5


Mass: 25634.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P40302, proteasome endopeptidase complex
#14: Protein PROTEASOME COMPONENT C1 / 20S PROTEASOME ALPHA SUBUNIT 7 / MACROPAIN SUBUNIT C1 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX ...20S PROTEASOME ALPHA SUBUNIT 7 / MACROPAIN SUBUNIT C1 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C1 / PROTEINASE YSCE SUBUNIT 1


Mass: 31575.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P21242, proteasome endopeptidase complex

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26S PROTEASE REGULATORY SUBUNIT ... , 5 types, 5 molecules HIJKM

#15: Protein 26S PROTEASE REGULATORY SUBUNIT 7 HOMOLOG / RPT1 / PROTEIN CIM5 / TAT-BINDING HOMOLOG 3


Mass: 52054.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P33299
#16: Protein 26S PROTEASE REGULATORY SUBUNIT 4 HOMOLOG / RPT2 / TAT-BINDING HOMOLOG 5


Mass: 48898.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P40327
#17: Protein 26S PROTEASE REGULATORY SUBUNIT 8 HOMOLOG / RPT6 / PROTEIN CIM3 / PROTEIN SUG1 / TAT-BINDING PROTEIN TBY1


Mass: 45342.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q01939
#18: Protein 26S PROTEASE REGULATORY SUBUNIT 6B HOMOLOG / RPT3 / PROTEIN YNT1 / TAT-BINDING HOMOLOG 2


Mass: 47953.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P33298
#20: Protein 26S PROTEASE REGULATORY SUBUNIT 6A / RPT5 / TAT-BINDING PROTEIN HOMOLOG 1 / TBP-1


Mass: 48315.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P33297

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Protein , 2 types, 2 molecules LY

#19: Protein 26S PROTEASE SUBUNIT RPT4 / RPT4 / 26S PROTEASE SUBUNIT SUG2 / PROTEASOMAL CAP SUBUNIT


Mass: 49480.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P53549
#32: Protein 26S PROTEASOME COMPLEX SUBUNIT SEM1


Mass: 10397.102 Da / Num. of mol.: 1 / Fragment: SEM1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: O94742

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26S PROTEASOME REGULATORY SUBUNIT ... , 12 types, 12 molecules NOPQRSTUVWXZ

#21: Protein 26S PROTEASOME REGULATORY SUBUNIT RPN2 / RPN2


Mass: 104351.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P32565
#22: Protein 26S PROTEASOME REGULATORY SUBUNIT RPN9 / RPN9 / PROTEASOME NON-ATPASE SUBUNIT 7


Mass: 45839.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q04062
#23: Protein 26S PROTEASOME REGULATORY SUBUNIT RPN5 / RPN5 / PROTEASOME NON-ATPASE SUBUNIT 5


Mass: 51840.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q12250
#24: Protein 26S PROTEASOME REGULATORY SUBUNIT RPN6 / RPN6 / PROTEASOME NON-ATPASE SUBUNIT 4


Mass: 49839.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q12377
#25: Protein 26S PROTEASOME REGULATORY SUBUNIT RPN7 / RPN7


Mass: 49016.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q06103
#26: Protein 26S PROTEASOME REGULATORY SUBUNIT RPN3 / RPN3


Mass: 60464.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P40016
#27: Protein 26S PROTEASOME REGULATORY SUBUNIT RPN12 / RPN12 / NUCLEAR INTEGRITY PROTEIN 1


Mass: 31952.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P32496
#28: Protein 26S PROTEASOME REGULATORY SUBUNIT RPN8 / RPN8


Mass: 38365.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q08723
#29: Protein 26S PROTEASOME REGULATORY SUBUNIT RPN11 / RPN11 / PROTEIN MPR1


Mass: 34442.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P43588
#30: Protein 26S PROTEASOME REGULATORY SUBUNIT RPN10 / RPN10


Mass: 29776.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P38886
#31: Protein 26S PROTEASOME REGULATORY SUBUNIT RPN13 / RPN13 / PROTEASOME NON-ATPASE SUBUNIT 13


Mass: 17919.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: O13563
#33: Protein 26S PROTEASOME REGULATORY SUBUNIT RPN1 / HMG-COA REDUCTASE DEGRADATION PROTEIN 2 / PROTEASOME NON-ATPASE SUBUNIT 1


Mass: 109601.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P38764

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Details

Sequence detailsLYS 108 ARG CONFLICT IN CHAIN 5 IS DUE TO A MUTATION IN THE STARTING MODEL PDB ENTRY 1RYP

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: 26S PROTEASOME / Type: COMPLEX
Buffer solutionpH: 7.1
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationCryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- HOMEMADE PLUNGER,

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Dec 24, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2 mm
Specimen holderTemperature: 80.5 K
Image recordingElectron dose: 25 e/Å2 / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k)

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Processing

EM softwareName: Xmipp / Category: 3D reconstruction
CTF correctionDetails: MICROGRAPH
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 8.8 Å / Num. of particles: 560000 / Nominal pixel size: 1.99 Å / Actual pixel size: 1.99 Å / Magnification calibration: FITTING OF 20S XTAL STRUCTURE
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2596 (DEPOSITION ID: 12358).
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: FSC / Details: METHOD--MDFF
RefinementHighest resolution: 8.8 Å
Refinement stepCycle: LAST / Highest resolution: 8.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms80139 0 0 0 80139

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