Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 34-mer - A2B2C2D2E2F2G2H2I2J2K2L2M2N2O1P1Q1R1S1T1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 34-mer - A28B5C1 

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

Macromolecule Content

• Total Structure Weight: 1049.26 kDa 
• Atom Count: 67692 
• Modelled Residue Count: 8637 
• Deposited Residue Count: 9401 
• Unique protein chains: 20

5L4G

The human 26S proteasome at 3.9 A

• DOI: 10.2210/pdb5L4G/pdb
• EMDataResource: EMD-4002

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: 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
Proteasome subunit alpha type-6	O [auth A], A [auth N]	246	Homo sapiens	Mutation(s): 0  Gene Names: PSMA6, PROS27 EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P60900 (Homo sapiens) Explore P60900  Go to UniProtKB:  P60900
PHAROS:  P60900 GTEx:  ENSG00000100902

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-2	P [auth B], B [auth O]	234	Homo sapiens	Mutation(s): 0  Gene Names: PSMA2, HC3, PSC3 EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P25787 (Homo sapiens) Explore P25787  Go to UniProtKB:  P25787
PHAROS:  P25787 GTEx:  ENSG00000106588

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-4	Q [auth C], C [auth P]	261	Homo sapiens	Mutation(s): 0  Gene Names: PSMA4, HC9, PSC9 EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P25789 (Homo sapiens) Explore P25789  Go to UniProtKB:  P25789
PHAROS:  P25789 GTEx:  ENSG00000041357

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-7	R [auth D], D [auth Q]	248	Homo sapiens	Mutation(s): 0  Gene Names: PSMA7, HSPC EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for O14818 (Homo sapiens) Explore O14818  Go to UniProtKB:  O14818
PHAROS:  O14818 GTEx:  ENSG00000101182

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-5	S [auth E], E [auth R]	241	Homo sapiens	Mutation(s): 0  Gene Names: PSMA5 EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P28066 (Homo sapiens) Explore P28066  Go to UniProtKB:  P28066
PHAROS:  P28066 GTEx:  ENSG00000143106

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-1	T [auth F], F [auth S]	263	Homo sapiens	Mutation(s): 0  Gene Names: PSMA1, HC2, NU, PROS30, PSC2 EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P25786 (Homo sapiens) Explore P25786  Go to UniProtKB:  P25786
PHAROS:  P25786 GTEx:  ENSG00000129084

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-3	U [auth G], G [auth T]	255	Homo sapiens	Mutation(s): 0  Gene Names: PSMA3, HC8, PSC8 EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P25788 (Homo sapiens) Explore P25788  Go to UniProtKB:  P25788
PHAROS:  P25788 GTEx:  ENSG00000100567

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-1	V [auth 1], H [auth U]	241	Homo sapiens	Mutation(s): 0  Gene Names: PSMB1, PSC5 EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P20618 (Homo sapiens) Explore P20618  Go to UniProtKB:  P20618
PHAROS:  P20618 GTEx:  ENSG00000008018

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-2	W [auth 2], I [auth V]	201	Homo sapiens	Mutation(s): 0  Gene Names: PSMB2 EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49721 (Homo sapiens) Explore P49721  Go to UniProtKB:  P49721
PHAROS:  P49721 GTEx:  ENSG00000126067

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-3	X [auth 3], J [auth W]	205	Homo sapiens	Mutation(s): 0  Gene Names: PSMB3 EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49720 (Homo sapiens) Explore P49720  Go to UniProtKB:  P49720
PHAROS:  P49720 GTEx:  ENSG00000277791

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-4	Y [auth 4], K [auth X]	264	Homo sapiens	Mutation(s): 0  Gene Names: PSMB4, PROS26 EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P28070 (Homo sapiens) Explore P28070  Go to UniProtKB:  P28070
PHAROS:  P28070 GTEx:  ENSG00000159377

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-5	Z [auth 5], L [auth Y]	263	Homo sapiens	Mutation(s): 0  Gene Names: PSMB5, LMPX, MB1, X EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P28074 (Homo sapiens) Explore P28074  Go to UniProtKB:  P28074
PHAROS:  P28074 GTEx:  ENSG00000100804

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-6	AA [auth 6], M [auth Z]	239	Homo sapiens	Mutation(s): 0  Gene Names: PSMB6, LMPY, Y EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P28072 (Homo sapiens) Explore P28072  Go to UniProtKB:  P28072
PHAROS:  P28072 GTEx:  ENSG00000142507

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-7	BA [auth 7], N [auth 8]	277	Homo sapiens	Mutation(s): 0  Gene Names: PSMB7, Z EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99436 (Homo sapiens) Explore Q99436  Go to UniProtKB:  Q99436
PHAROS:  Q99436 GTEx:  ENSG00000136930

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
26S protease regulatory subunit 7	CA [auth H]	433	Homo sapiens	Mutation(s): 0  Gene Names: PSMC2, MSS1
UniProt & NIH Common Fund Data Resources
Find proteins for P35998 (Homo sapiens) Explore P35998  Go to UniProtKB:  P35998
PHAROS:  P35998 GTEx:  ENSG00000161057

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
26S protease regulatory subunit 4	DA [auth I]	440	Homo sapiens	Mutation(s): 0  Gene Names: PSMC1
UniProt & NIH Common Fund Data Resources
Find proteins for P62191 (Homo sapiens) Explore P62191  Go to UniProtKB:  P62191
GTEx:  ENSG00000100764

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
26S protease regulatory subunit 6B	EA [auth K]	418	Homo sapiens	Mutation(s): 0  Gene Names: PSMC4, MIP224, TBP7
UniProt & NIH Common Fund Data Resources
Find proteins for P43686 (Homo sapiens) Explore P43686  Go to UniProtKB:  P43686
PHAROS:  P43686 GTEx:  ENSG00000013275

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
26S protease regulatory subunit 10B	FA [auth L]	389	Homo sapiens	Mutation(s): 0  Gene Names: PSMC6, SUG2
UniProt & NIH Common Fund Data Resources
Find proteins for P62333 (Homo sapiens) Explore P62333  Go to UniProtKB:  P62333
PHAROS:  P62333

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
26S protease regulatory subunit 6A	GA [auth M]	439	Homo sapiens	Mutation(s): 0  Gene Names: PSMC3, TBP1
UniProt & NIH Common Fund Data Resources
Find proteins for P17980 (Homo sapiens) Explore P17980  Go to UniProtKB:  P17980
PHAROS:  P17980 GTEx:  ENSG00000165916

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
26S protease regulatory subunit 8	HA [auth J]	406	Homo sapiens	Mutation(s): 0  Gene Names: PSMC5, SUG1
UniProt & NIH Common Fund Data Resources
Find proteins for P62195 (Homo sapiens) Explore P62195  Go to UniProtKB:  P62195
PHAROS:  P62195 GTEx:  ENSG00000087191

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	IA [auth H], KA [auth I], MA [auth K], OA [auth L], QA [auth M]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP	SA [auth J]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	JA [auth H], LA [auth I], NA [auth K], PA [auth L], RA [auth M]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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, Derived calculations
• Version 1.3: 2019-12-11
  Changes: Other