5LN3

The human 26S Proteasome at 6.8 Ang.

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Molecular Details Underlying Dynamic Structures and Regulation of the Human 26S Proteasome.

Wang, X., Cimermancic, P., Yu, C., Schweitzer, A., Chopra, N., Engel, J.L., Greenberg, C., Huszagh, A.S., Beck, F., Sakata, E., Yang, Y., Novitsky, E.J., Leitner, A., Nanni, P., Kahraman, A., Guo, X., Dixon, J.E., Rychnovsky, S.D., Aebersold, R., Baumeister, W., Sali, A., Huang, L.

(2017) Mol. Cell Proteomics 16: 840-854

  • DOI: 10.1074/mcp.M116.065326

  • PubMed Abstract: 

    • The 26S proteasome is the macromolecular machine responsible for ATP/ubiquitin dependent degradation. As aberration in proteasomal degradation has been implicated in many human diseases, structural analysis of the human 26S proteasome complex is esse ...

    The 26S proteasome is the macromolecular machine responsible for ATP/ubiquitin dependent degradation. As aberration in proteasomal degradation has been implicated in many human diseases, structural analysis of the human 26S proteasome complex is essential to advance our understanding of its action and regulation mechanisms. In recent years, cross-linking mass spectrometry (XL-MS) has emerged as a powerful tool for elucidating structural topologies of large protein assemblies, with its unique capability of studying protein complexes in cells. To facilitate the identification of cross-linked peptides, we have previously developed a robust amine reactive sulfoxide-containing MS-cleavable cross-linker, disuccinimidyl sulfoxide (DSSO). To better understand the structure and regulation of the human 26S proteasome, we have established new DSSO-based in vivo and in vitro XL-MS workflows by coupling with HB-tag based affinity purification to comprehensively examine protein-protein interactions within the 26S proteasome. In total, we have identified 447 unique lysine-to-lysine linkages delineating 67 interprotein and 26 intraprotein interactions, representing the largest cross-link dataset for proteasome complexes. In combination with EM maps and computational modeling, the architecture of the 26S proteasome was determined to infer its structural dynamics. In particular, three proteasome subunits Rpn1, Rpn6, and Rpt6 displayed multiple conformations that have not been previously reported. Additionally, cross-links between proteasome subunits and 15 proteasome interacting proteins including 9 known and 6 novel ones have been determined to demonstrate their physical interactions at the amino acid level. Our results have provided new insights on the dynamics of the 26S human proteasome and the methodologies presented here can be applied to study other protein complexes.

    Organizational Affiliation: 

    From the ‡Department of Physiology & Biophysics, University of California, Irvine, Irvine, California 92697.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 2
Z
908Homo sapiensMutation(s): 0 
Gene Names: PSMD2 (TRAP2)
Find proteins for Q13200 (Homo sapiens)
Go to Gene View: PSMD2
Go to UniProtKB:  Q13200
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-6
1
239Homo sapiensMutation(s): 0 
Gene Names: PSMB6 (LMPY, Y)
EC: 3.4.25.1
Find proteins for P28072 (Homo sapiens)
Go to Gene View: PSMB6
Go to UniProtKB:  P28072
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-7
2
277Homo sapiensMutation(s): 0 
Gene Names: PSMB7 (Z)
EC: 3.4.25.1
Find proteins for Q99436 (Homo sapiens)
Go to Gene View: PSMB7
Go to UniProtKB:  Q99436
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-3
3
205Homo sapiensMutation(s): 0 
Gene Names: PSMB3
EC: 3.4.25.1
Find proteins for P49720 (Homo sapiens)
Go to Gene View: PSMB3
Go to UniProtKB:  P49720
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-2
4
201Homo sapiensMutation(s): 0 
Gene Names: PSMB2
EC: 3.4.25.1
Find proteins for P49721 (Homo sapiens)
Go to Gene View: PSMB2
Go to UniProtKB:  P49721
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-5
5
263Homo sapiensMutation(s): 0 
Gene Names: PSMB5 (LMPX, MB1, X)
EC: 3.4.25.1
Find proteins for P28074 (Homo sapiens)
Go to Gene View: PSMB5
Go to UniProtKB:  P28074
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-1
6
241Homo sapiensMutation(s): 0 
Gene Names: PSMB1 (PSC5)
EC: 3.4.25.1
Find proteins for P20618 (Homo sapiens)
Go to Gene View: PSMB1
Go to UniProtKB:  P20618
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-4
7
264Homo sapiensMutation(s): 0 
Gene Names: PSMB4 (PROS26)
EC: 3.4.25.1
Find proteins for P28070 (Homo sapiens)
Go to Gene View: PSMB4
Go to UniProtKB:  P28070
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-6
A
246Homo sapiensMutation(s): 0 
Gene Names: PSMA6 (PROS27)
EC: 3.4.25.1
Find proteins for P60900 (Homo sapiens)
Go to Gene View: PSMA6
Go to UniProtKB:  P60900
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-2
B
234Homo sapiensMutation(s): 0 
Gene Names: PSMA2 (HC3, PSC3)
EC: 3.4.25.1
Find proteins for P25787 (Homo sapiens)
Go to Gene View: PSMA2
Go to UniProtKB:  P25787
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-4
C
261Homo sapiensMutation(s): 0 
Gene Names: PSMA4 (HC9, PSC9)
EC: 3.4.25.1
Find proteins for P25789 (Homo sapiens)
Go to Gene View: PSMA4
Go to UniProtKB:  P25789
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-7
D
248Homo sapiensMutation(s): 0 
Gene Names: PSMA7 (HSPC)
EC: 3.4.25.1
Find proteins for O14818 (Homo sapiens)
Go to Gene View: PSMA7
Go to UniProtKB:  O14818
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-5
E
241Homo sapiensMutation(s): 0 
Gene Names: PSMA5
EC: 3.4.25.1
Find proteins for P28066 (Homo sapiens)
Go to Gene View: PSMA5
Go to UniProtKB:  P28066
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-1
F
263Homo sapiensMutation(s): 0 
Gene Names: PSMA1 (HC2, NU, PROS30, PSC2)
EC: 3.4.25.1
Find proteins for P25786 (Homo sapiens)
Go to Gene View: PSMA1
Go to UniProtKB:  P25786
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-3
G
255Homo sapiensMutation(s): 0 
Gene Names: PSMA3 (HC8, PSC8)
EC: 3.4.25.1
Find proteins for P25788 (Homo sapiens)
Go to Gene View: PSMA3
Go to UniProtKB:  P25788
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
26S protease regulatory subunit 7
H
433Homo sapiensMutation(s): 0 
Gene Names: PSMC2 (MSS1)
Find proteins for P35998 (Homo sapiens)
Go to Gene View: PSMC2
Go to UniProtKB:  P35998
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
26S protease regulatory subunit 4
I
440Homo sapiensMutation(s): 0 
Gene Names: PSMC1
Find proteins for P62191 (Homo sapiens)
Go to Gene View: PSMC1
Go to UniProtKB:  P62191
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
26S protease regulatory subunit 8
J
406Homo sapiensMutation(s): 0 
Gene Names: PSMC5 (SUG1)
Find proteins for P62195 (Homo sapiens)
Go to Gene View: PSMC5
Go to UniProtKB:  P62195
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
26S protease regulatory subunit 6B
K
418Homo sapiensMutation(s): 0 
Gene Names: PSMC4 (MIP224, TBP7)
Find proteins for P43686 (Homo sapiens)
Go to Gene View: PSMC4
Go to UniProtKB:  P43686
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
26S protease regulatory subunit 10B
L
389Homo sapiensMutation(s): 0 
Gene Names: PSMC6 (SUG2)
Find proteins for P62333 (Homo sapiens)
Go to Gene View: PSMC6
Go to UniProtKB:  P62333
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
26S protease regulatory subunit 6A
M
439Homo sapiensMutation(s): 0 
Gene Names: PSMC3 (TBP1)
Find proteins for P17980 (Homo sapiens)
Go to Gene View: PSMC3
Go to UniProtKB:  P17980
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 1
N
953Homo sapiensMutation(s): 0 
Gene Names: PSMD1
Find proteins for Q99460 (Homo sapiens)
Go to Gene View: PSMD1
Go to UniProtKB:  Q99460
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 13
O
376Homo sapiensMutation(s): 0 
Gene Names: PSMD13
Find proteins for Q9UNM6 (Homo sapiens)
Go to Gene View: PSMD13
Go to UniProtKB:  Q9UNM6
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 12
P
456Homo sapiensMutation(s): 0 
Gene Names: PSMD12
Find proteins for O00232 (Homo sapiens)
Go to Gene View: PSMD12
Go to UniProtKB:  O00232
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 11
Q
422Homo sapiensMutation(s): 0 
Gene Names: PSMD11
Find proteins for O00231 (Homo sapiens)
Go to Gene View: PSMD11
Go to UniProtKB:  O00231
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 6
R
389Homo sapiensMutation(s): 0 
Gene Names: PSMD6 (KIAA0107, PFAAP4)
Find proteins for Q15008 (Homo sapiens)
Go to Gene View: PSMD6
Go to UniProtKB:  Q15008
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 3
S
534Homo sapiensMutation(s): 0 
Gene Names: PSMD3
Find proteins for O43242 (Homo sapiens)
Go to Gene View: PSMD3
Go to UniProtKB:  O43242
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 8
T
350Homo sapiensMutation(s): 0 
Gene Names: PSMD8
Find proteins for P48556 (Homo sapiens)
Go to Gene View: PSMD8
Go to UniProtKB:  P48556
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 7
U
324Homo sapiensMutation(s): 0 
Gene Names: PSMD7 (MOV34L)
Find proteins for P51665 (Homo sapiens)
Go to Gene View: PSMD7
Go to UniProtKB:  P51665
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 14
V
310Homo sapiensMutation(s): 0 
Gene Names: PSMD14 (POH1)
EC: 3.4.19.-
Find proteins for O00487 (Homo sapiens)
Go to Gene View: PSMD14
Go to UniProtKB:  O00487
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 4
W
377Homo sapiensMutation(s): 0 
Gene Names: PSMD4 (MCB1)
Find proteins for P55036 (Homo sapiens)
Go to Gene View: PSMD4
Go to UniProtKB:  P55036
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
26S proteasome complex subunit DSS1
Y
70Homo sapiensMutation(s): 0 
Gene Names: SEM1 (C7orf76, DSS1, SHFDG1, SHFM1)
Find proteins for P60896 (Homo sapiens)
Go to Gene View: SEM1
Go to UniProtKB:  P60896
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2017-04-12
    Type: Database references
  • Version 1.2: 2017-05-24
    Type: Database references