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- PDB-5a5b: Structure of the 26S proteasome-Ubp6 complex -

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Basic information

Entry
Database: PDB / ID: 5a5b
TitleStructure of the 26S proteasome-Ubp6 complex
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
  • UBIQUITIN ALDEHYDE
  • UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 6
KeywordsHYDROLASE / CONFORMATIONAL SWITCHING / PROTEIN DEGRADATION / PROTEOSTASIS / QUALITY CONTROL / UBP6 / USP14
Function / homology
Function and homology information


SAGA complex localization to transcription regulatory region / Metalloprotease DUBs / negative regulation of proteasomal protein catabolic process / peroxisome fission / mitochondria-associated ubiquitin-dependent protein catabolic process / regulation of proteasomal ubiquitin-dependent protein catabolic process / proteasome storage granule assembly / transcription export complex 2 / proteasome regulatory particle assembly / protein deneddylation ...SAGA complex localization to transcription regulatory region / Metalloprotease DUBs / negative regulation of proteasomal protein catabolic process / peroxisome fission / mitochondria-associated ubiquitin-dependent protein catabolic process / regulation of proteasomal ubiquitin-dependent protein catabolic process / 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 / Peptide chain elongation / Selenocysteine synthesis / Antigen processing: Ubiquitination & Proteasome degradation / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / endopeptidase activator activity / polyubiquitin modification-dependent protein binding / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / proteasome assembly / protein deubiquitination / positive regulation of RNA polymerase II transcription preinitiation complex assembly / L13a-mediated translational silencing of Ceruloplasmin expression / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / Major pathway of rRNA processing in the nucleolus and cytosol / Ub-specific processing proteases / threonine-type endopeptidase activity / mRNA export from nucleus / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / regulation of proteasomal protein catabolic process / enzyme regulator activity / ERAD pathway / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / protein folding chaperone / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Neutrophil degranulation / Glycogen synthesis / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / cytosolic ribosome / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / VLDLR internalisation and degradation / Downregulation of ERBB4 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A
Similarity search - Function
Ubiquitin carboxyl-terminal hydrolase 14-like / 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 ...Ubiquitin carboxyl-terminal hydrolase 14-like / 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 / Ubiquitin specific protease (USP) domain signature 2. / : / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) 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 / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / AAA ATPase, AAA+ lid domain
Similarity search - Domain/homology
26S proteasome regulatory subunit RPN13 / 26S proteasome complex subunit SEM1 / Polyubiquitin-C / 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 ...26S proteasome regulatory subunit RPN13 / 26S proteasome complex subunit SEM1 / Polyubiquitin-C / 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 / Ubiquitin carboxyl-terminal hydrolase 6 / 26S proteasome subunit RPT4 / Ubiquitin-ribosomal protein eL40 fusion protein / 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)
HOMO SAPIENS (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.5 Å
AuthorsAufderheide, A. / Beck, F. / Stengel, F. / Hartwig, M. / Schweitzer, A. / Pfeifer, G. / Goldberg, A.L. / Sakata, E. / Baumeister, W. / Foerster, F.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2015
Title: Structural characterization of the interaction of Ubp6 with the 26S proteasome.
Authors: Antje Aufderheide / Florian Beck / Florian Stengel / Michaela Hartwig / Andreas Schweitzer / Günter Pfeifer / Alfred L Goldberg / Eri Sakata / Wolfgang Baumeister / Friedrich Förster /
Abstract: In eukaryotic cells, the 26S proteasome is responsible for the regulated degradation of intracellular proteins. Several cofactors interact transiently with this large macromolecular machine and ...In eukaryotic cells, the 26S proteasome is responsible for the regulated degradation of intracellular proteins. Several cofactors interact transiently with this large macromolecular machine and modulate its function. The deubiquitylating enzyme ubiquitin C-terminal hydrolase 6 [Ubp6; ubiquitin-specific protease (USP) 14 in mammals] is the most abundant proteasome-interacting protein and has multiple roles in regulating proteasome function. Here, we investigate the structural basis of the interaction between Ubp6 and the 26S proteasome in the presence and absence of the inhibitor ubiquitin aldehyde. To this end we have used single-particle electron cryomicroscopy in combination with cross-linking and mass spectrometry. Ubp6 binds to the regulatory particle non-ATPase (Rpn) 1 via its N-terminal ubiquitin-like domain, whereas its catalytic USP domain is positioned variably. Addition of ubiquitin aldehyde stabilizes the binding of the USP domain in a position where it bridges the proteasome subunits Rpn1 and the regulatory particle triple-A ATPase (Rpt) 1. The USP domain binds to Rpt1 in the immediate vicinity of the Ubp6 active site, which may effect its activation. The catalytic triad is positioned in proximity to the mouth of the ATPase module and to the deubiquitylating enzyme Rpn11, strongly implying their functional linkage. On the proteasome side, binding of Ubp6 favors conformational switching of the 26S proteasome into an intermediate-energy conformational state, in particular upon the addition of ubiquitin aldehyde. This modulation of the conformational space of the 26S proteasome by Ubp6 explains the effects of Ubp6 on the kinetics of proteasomal degradation.
History
DepositionJun 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Oct 21, 2015Group: Other
Revision 1.3Aug 30, 2017Group: Data collection / Refinement description / Category: em_3d_fitting / em_image_scans / em_software
Item: _em_3d_fitting.target_criteria / _em_software.image_processing_id / _em_software.name
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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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
8: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 6
9: UBIQUITIN ALDEHYDE
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)1,366,67035
Polymers1,366,67035
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by 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
#10: 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
#11: 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
#12: 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
#13: 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
#14: 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
#15: 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
#16: 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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Protein , 4 types, 4 molecules 89LY

#8: Protein UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 6


Mass: 48825.488 Da / Num. of mol.: 1 / Fragment: RESIDUES 97-499 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: YFR010W / References: UniProt: P43593, EC: 3.1.2.15
#9: Protein UBIQUITIN ALDEHYDE


Mass: 8560.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P0CG48, UniProt: P62987*PLUS
#21: 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
#34: 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 PROTEASE REGULATORY SUBUNIT ... , 5 types, 5 molecules HIJKM

#17: 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
#18: 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
#19: 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
#20: 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
#22: 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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26S PROTEASOME REGULATORY SUBUNIT ... , 12 types, 12 molecules NOPQRSTUVWXZ

#23: 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
#24: 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
#25: 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
#26: 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
#27: 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
#28: 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
#29: 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
#30: 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
#31: 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
#32: 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
#33: 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
#35: 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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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 FROM SACCHAROMYCES CEREVISIAE IN THE PRESENCE OF SACCHAROMYCES CEREVISIAE UBP6 AND UBIQUITIN ALDEHYDE
Type: COMPLEX / Details: MICROGRAPHS SELECTED BY POWER SPECTRA
SpecimenConc.: 0.35 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen 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 12, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2 mm
Specimen holderTilt angle max: 0 °
Image recordingElectron dose: 45 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM softwareName: Xmipp / Category: 3D reconstruction
CTF correctionDetails: MICROGRAPH
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: PROJECTION MATCHING WITH A GOLD- -STANDARD PROCEDURE
Resolution: 9.5 Å / Resolution method: FSC / Num. of particles: 53000 / Nominal pixel size: 1.99 Å / Actual pixel size: 1.99 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3034. (DEPOSITION ID: 13439).
Refinement type: HALF-MAPS REFINED INDEPENDENTLY / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: Cross-correlation coefficient / Details: METHOD--LOCAL CORRELATION
Atomic model building
IDPDB-ID 3D fitting-ID
14C43

4c43

1
21VJV

1vjv

1
RefinementHighest resolution: 9.5 Å
Refinement stepCycle: LAST / Highest resolution: 9.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms83704 0 0 0 83704

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