Biological Assembly 1  

 3D View: Structure

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 12-mer - A1B1C1D1E1F1G1H1I1J1K1L1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 12-mer - A2B1C1D1E1F1G1H1I1J1K1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 616.87 kDa 
• Atom Count: 39659 
• Modelled Residue Count: 5000 
• Deposited Residue Count: 5469 
• Unique protein chains: 12

5L4K

The human 26S proteasome lid

• DOI: 10.2210/pdb5L4K/pdb
• EMDataResource: EMD-4002

• Classification: STRUCTURAL PROTEIN
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2016-05-25 Released: 2016-09-07 
• Deposition Author(s): Schweitzer, A., Aufderheide, A., Rudack, T., Beck, F.

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Experimental Data Snapshot

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

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

• PubMed: 27342858 
• 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. 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.

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Organizational Affiliation: 

Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, D-82152 Martinsried, Germany; [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 4	A [auth W]	377	Homo sapiens	Mutation(s): 0  Gene Names: PSMD4, MCB1
Find proteins for P55036 (Homo sapiens) Explore P55036  Go to UniProtKB:  P55036
NIH Common Fund Data Resources
PHAROS:  P55036 GTEx:  ENSG00000159352

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 14	B [auth V]	310	Homo sapiens	Mutation(s): 0  Gene Names: PSMD14, POH1 EC: 3.4.19
Find proteins for O00487 (Homo sapiens) Explore O00487  Go to UniProtKB:  O00487
NIH Common Fund Data Resources
PHAROS:  O00487 GTEx:  ENSG00000115233

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 8	C [auth T]	350	Homo sapiens	Mutation(s): 0  Gene Names: PSMD8
Find proteins for P48556 (Homo sapiens) Explore P48556  Go to UniProtKB:  P48556
NIH Common Fund Data Resources
PHAROS:  P48556 GTEx:  ENSG00000099341

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome complex subunit DSS1	D [auth Y]	70	Homo sapiens	Mutation(s): 0  Gene Names: SEM1, C7orf76, DSS1, SHFDG1, SHFM1
Find proteins for P60896 (Homo sapiens) Explore P60896  Go to UniProtKB:  P60896
NIH Common Fund Data Resources
PHAROS:  P60896 GTEx:  ENSG00000127922

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 2	E [auth Z]	908	Homo sapiens	Mutation(s): 0  Gene Names: PSMD2, TRAP2
Find proteins for Q13200 (Homo sapiens) Explore Q13200  Go to UniProtKB:  Q13200
NIH Common Fund Data Resources
PHAROS:  Q13200 GTEx:  ENSG00000175166

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 1	F [auth N]	953	Homo sapiens	Mutation(s): 0  Gene Names: PSMD1
Find proteins for Q99460 (Homo sapiens) Explore Q99460  Go to UniProtKB:  Q99460
NIH Common Fund Data Resources
PHAROS:  Q99460 GTEx:  ENSG00000173692

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 3	G [auth S]	534	Homo sapiens	Mutation(s): 0  Gene Names: PSMD3
Find proteins for O43242 (Homo sapiens) Explore O43242  Go to UniProtKB:  O43242
NIH Common Fund Data Resources
PHAROS:  O43242 GTEx:  ENSG00000108344

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 12	H [auth P]	456	Homo sapiens	Mutation(s): 0  Gene Names: PSMD12
Find proteins for O00232 (Homo sapiens) Explore O00232  Go to UniProtKB:  O00232
NIH Common Fund Data Resources
PHAROS:  O00232 GTEx:  ENSG00000197170

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 11	I [auth Q]	422	Homo sapiens	Mutation(s): 0  Gene Names: PSMD11
Find proteins for O00231 (Homo sapiens) Explore O00231  Go to UniProtKB:  O00231
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PHAROS:  O00231 GTEx:  ENSG00000108671

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 6	J [auth R]	389	Homo sapiens	Mutation(s): 0  Gene Names: PSMD6, KIAA0107, PFAAP4
Find proteins for Q15008 (Homo sapiens) Explore Q15008  Go to UniProtKB:  Q15008
NIH Common Fund Data Resources
PHAROS:  Q15008 GTEx:  ENSG00000163636

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 7	K [auth U]	324	Homo sapiens	Mutation(s): 0  Gene Names: PSMD7, MOV34L
Find proteins for P51665 (Homo sapiens) Explore P51665  Go to UniProtKB:  P51665
NIH Common Fund Data Resources
PHAROS:  P51665 GTEx:  ENSG00000103035

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 13	L [auth O]	376	Homo sapiens	Mutation(s): 0  Gene Names: PSMD13
Find proteins for Q9UNM6 (Homo sapiens) Explore Q9UNM6  Go to UniProtKB:  Q9UNM6
NIH Common Fund Data Resources
PHAROS:  Q9UNM6 GTEx:  ENSG00000185627

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-05-25 
• Released Date: 2016-09-07 
Deposition Author(s): Schweitzer, A., Aufderheide, A., Rudack, T., Beck, F.

Revision History  

• 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