5A5B

Structure of the 26S proteasome-Ubp6 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Characterization of the Interaction of Ubp6 with the 26S Proteasome.

Aufderheide, A.Beck, F.Stengel, F.Hartwig, M.Schweitzer, A.Pfeifer, G.Goldberg, A.L.Sakata, E.Baumeister, W.Forster, F.

(2015) Proc.Natl.Acad.Sci.USA 112: 8626

  • DOI: 10.1073/pnas.1510449112

  • PubMed 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 modulate its function. The deubiquitylating enzyme ubiqu ...

    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.


    Organizational Affiliation

    Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME COMPONENT PRE3
1
215Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRE3
EC: 3.4.25.1
Find proteins for P38624 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38624
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME COMPONENT PUP1
2
261Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PUP1
EC: 3.4.25.1
Find proteins for P25043 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME COMPONENT PUP3
3
205Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PUP3
EC: 3.4.25.1
Find proteins for P25451 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME COMPONENT C11
4
198Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRE1
EC: 3.4.25.1
Find proteins for P22141 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P22141
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME COMPONENT PRE2
5
287Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRE2 (DOA3, PRG1)
EC: 3.4.25.1
Find proteins for P30656 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME COMPONENT C5
6
241Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRE7 (PRS3, PTS1)
EC: 3.4.25.1
Find proteins for P23724 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME COMPONENT PRE4
7
266Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRE4
EC: 3.4.25.1
Find proteins for P30657 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 6
8
416Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: UBP6
EC: 3.4.19.12
Find proteins for P43593 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
UBIQUITIN ALDEHYDE
9
76Homo sapiensGene Names: UBA52 (UBCEP2)
Find proteins for P62987 (Homo sapiens)
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Go to UniProtKB:  P62987
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME COMPONENT C7-ALPHA
A
252Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SCL1 (PRC2, PRS2)
EC: 3.4.25.1
Find proteins for P21243 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME COMPONENT Y7
B
250Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRE8 (PRS4)
EC: 3.4.25.1
Find proteins for P23639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME COMPONENT Y13
C
258Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRE9 (PRS5)
EC: 3.4.25.1
Find proteins for P23638 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME COMPONENT PRE6
D
254Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRE6
EC: 3.4.25.1
Find proteins for P40303 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME COMPONENT PUP2
E
260Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PUP2 (DOA5)
EC: 3.4.25.1
Find proteins for P32379 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME COMPONENT PRE5
F
234Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRE5
EC: 3.4.25.1
Find proteins for P40302 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME COMPONENT C1
G
288Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRE10 (PRC1, PRS1)
EC: 3.4.25.1
Find proteins for P21242 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
26S PROTEASE REGULATORY SUBUNIT 7 HOMOLOG
H
467Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPT1 (CIM5, YTA3)
Find proteins for P33299 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
26S PROTEASE REGULATORY SUBUNIT 4 HOMOLOG
I
437Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPT2 (YHS4, YTA5)
Find proteins for P40327 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
26S PROTEASE REGULATORY SUBUNIT 8 HOMOLOG
J
405Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPT6 (CIM3, CRL3, SUG1, TBPY, TBY1)
Find proteins for Q01939 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q01939
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
26S PROTEASE REGULATORY SUBUNIT 6B HOMOLOG
K
428Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPT3 (YNT1, YTA2)
Find proteins for P33298 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
26S PROTEASE SUBUNIT RPT4
L
437Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPT4 (CRL13, PCS1, SUG2)
Find proteins for P53549 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
26S PROTEASE REGULATORY SUBUNIT 6A
M
434Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPT5 (YTA1)
Find proteins for P33297 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
26S PROTEASOME REGULATORY SUBUNIT RPN2
N
945Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPN2 (SEN3)
Find proteins for P32565 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPN2
Go to UniProtKB:  P32565
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
26S PROTEASOME REGULATORY SUBUNIT RPN9
O
393Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPN9 (NAS7)
Find proteins for Q04062 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q04062
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
26S PROTEASOME REGULATORY SUBUNIT RPN5
P
445Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPN5 (NAS5)
Find proteins for Q12250 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
26S PROTEASOME REGULATORY SUBUNIT RPN6
Q
434Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPN6 (NAS4)
Find proteins for Q12377 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
26S PROTEASOME REGULATORY SUBUNIT RPN7
R
429Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPN7
Find proteins for Q06103 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
26S PROTEASOME REGULATORY SUBUNIT RPN3
S
523Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPN3 (SUN2)
Find proteins for P40016 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
26S PROTEASOME REGULATORY SUBUNIT RPN12
T
274Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPN12 (NIN1)
Find proteins for P32496 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
26S PROTEASOME REGULATORY SUBUNIT RPN8
U
338Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPN8
Find proteins for Q08723 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
26S PROTEASOME REGULATORY SUBUNIT RPN11
V
306Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPN11 (MPR1)
EC: 3.4.19.12
Find proteins for P43588 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
26S PROTEASOME REGULATORY SUBUNIT RPN10
W
268Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPN10 (MCB1, SUN1)
Find proteins for P38886 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
26S PROTEASOME REGULATORY SUBUNIT RPN13
X
156Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPN13 (DAQ1)
Find proteins for O13563 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
26S PROTEASOME COMPLEX SUBUNIT SEM1
Y
89Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SEM1 (DSH1)
Find proteins for O94742 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  O94742
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
26S PROTEASOME REGULATORY SUBUNIT RPN1
Z
993Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPN1 (HRD2, NAS1, RPD1)
Find proteins for P38764 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPN1
Go to UniProtKB:  P38764
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
GLZ
Query on GLZ
9
L-PEPTIDE LINKINGC2 H5 N OGLY
MSE
Query on MSE
8
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-22
    Type: Initial release
  • Version 1.1: 2015-07-29
    Type: Database references
  • Version 1.2: 2015-10-21
    Type: Other
  • Version 1.3: 2017-08-30
    Type: Data collection, Refinement description