5L4K

The human 26S proteasome lid

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 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

Structure of the human 26S proteasome at a resolution of 3.9 angstrom.

Schweitzer, A., Aufderheide, A., Rudack, T., Beck, F., Pfeifer, G., Plitzko, J.M., Sakata, E., Schulten, K., Forster, F., Baumeister, W.

(2016) Proc Natl Acad Sci U S A 113: 7816-7821

  • DOI: 10.1073/pnas.1608050113
  • Primary Citation of Related Structures:  
    5L4G, 5L4K

  • PubMed Abstract: 

    • Protein degradation in eukaryotic cells is performed by the Ubiquitin-Proteasome System (UPS). The 26S proteasome holocomplex consists of a core particle (CP) that proteolytically degrades polyubiquitylated proteins, and a regulatory particle (RP) containing the AAA-ATPase module ...

    Protein degradation in eukaryotic cells is performed by the Ubiquitin-Proteasome System (UPS). The 26S proteasome holocomplex consists of a core particle (CP) that proteolytically degrades polyubiquitylated proteins, and a regulatory particle (RP) containing the AAA-ATPase module. This module controls access to the proteolytic chamber inside the CP and is surrounded by non-ATPase subunits (Rpns) that recognize substrates and deubiquitylate them before unfolding and degradation. The architecture of the 26S holocomplex is highly conserved between yeast and humans. The structure of the human 26S holocomplex described here reveals previously unidentified features of the AAA-ATPase heterohexamer. One subunit, Rpt6, has ADP bound, whereas the other five have ATP in their binding pockets. Rpt6 is structurally distinct from the other five Rpt subunits, most notably in its pore loop region. For Rpns, the map reveals two main, previously undetected, features: the C terminus of Rpn3 protrudes into the mouth of the ATPase ring; and Rpn1 and Rpn2, the largest proteasome subunits, are linked by an extended connection. The structural features of the 26S proteasome observed in this study are likely to be important for coordinating the proteasomal subunits during substrate processing.

    Organizational Affiliation: 

    Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, D-82152 Martinsried, Germany; f.g.forster@uu.nl baumeist@biochem.mpg.de.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 4A [auth W]377Homo sapiensMutation(s): 0 
Gene Names: PSMD4, MCB1
UniProt & NIH Common Fund Data Resources
Find proteins for P55036 (Homo sapiens)
Explore P55036 
Go to UniProtKB:  P55036
PHAROS:  P55036
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55036
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 14B [auth V]310Homo sapiensMutation(s): 0 
Gene Names: PSMD14, POH1
EC: 3.4.19
UniProt & NIH Common Fund Data Resources
Find proteins for O00487 (Homo sapiens)
Explore O00487 
Go to UniProtKB:  O00487
PHAROS:  O00487
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00487
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 8C [auth T]350Homo sapiensMutation(s): 0 
Gene Names: PSMD8
UniProt & NIH Common Fund Data Resources
Find proteins for P48556 (Homo sapiens)
Explore P48556 
Go to UniProtKB:  P48556
PHAROS:  P48556
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48556
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome complex subunit DSS1D [auth Y]70Homo sapiensMutation(s): 0 
Gene Names: SEM1, C7orf76, DSS1, SHFDG1, SHFM1
UniProt & NIH Common Fund Data Resources
Find proteins for P60896 (Homo sapiens)
Explore P60896 
Go to UniProtKB:  P60896
PHAROS:  P60896
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60896
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 2E [auth Z]908Homo sapiensMutation(s): 0 
Gene Names: PSMD2, TRAP2
UniProt & NIH Common Fund Data Resources
Find proteins for Q13200 (Homo sapiens)
Explore Q13200 
Go to UniProtKB:  Q13200
PHAROS:  Q13200
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13200
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 1F [auth N]953Homo sapiensMutation(s): 0 
Gene Names: PSMD1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99460 (Homo sapiens)
Explore Q99460 
Go to UniProtKB:  Q99460
PHAROS:  Q99460
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99460
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 3G [auth S]534Homo sapiensMutation(s): 0 
Gene Names: PSMD3
UniProt & NIH Common Fund Data Resources
Find proteins for O43242 (Homo sapiens)
Explore O43242 
Go to UniProtKB:  O43242
PHAROS:  O43242
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43242
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 12H [auth P]456Homo sapiensMutation(s): 0 
Gene Names: PSMD12
UniProt & NIH Common Fund Data Resources
Find proteins for O00232 (Homo sapiens)
Explore O00232 
Go to UniProtKB:  O00232
PHAROS:  O00232
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00232
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 11I [auth Q]422Homo sapiensMutation(s): 0 
Gene Names: PSMD11
UniProt & NIH Common Fund Data Resources
Find proteins for O00231 (Homo sapiens)
Explore O00231 
Go to UniProtKB:  O00231
PHAROS:  O00231
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00231
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 6J [auth R]389Homo sapiensMutation(s): 0 
Gene Names: PSMD6, KIAA0107, PFAAP4
UniProt & NIH Common Fund Data Resources
Find proteins for Q15008 (Homo sapiens)
Explore Q15008 
Go to UniProtKB:  Q15008
PHAROS:  Q15008
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15008
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 7K [auth U]324Homo sapiensMutation(s): 0 
Gene Names: PSMD7, MOV34L
UniProt & NIH Common Fund Data Resources
Find proteins for P51665 (Homo sapiens)
Explore P51665 
Go to UniProtKB:  P51665
PHAROS:  P51665
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51665
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 13L [auth O]376Homo sapiensMutation(s): 0 
Gene Names: PSMD13
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNM6 (Homo sapiens)
Explore Q9UNM6 
Go to UniProtKB:  Q9UNM6
PHAROS:  Q9UNM6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UNM6
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-07
    Type: Initial release
  • Version 1.1: 2016-09-21
    Changes: Database references
  • Version 1.2: 2017-08-02
    Changes: Data collection
  • Version 1.3: 2019-12-11
    Changes: Other