› 5ln3

Electron Microscopy
6.8Å resolution

The human 26S Proteasome at 6.8 Ang.

Released:
DOI: 10.2210/pdb5ln3/pdb
PDB entry 5ln3 coloured by chain, front view.
PDB entry 5ln3 coloured by chain, side view.
PDB entry 5ln3 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Molecular Details Underlying Dynamic Structures and Regulation of the Human 26S Proteasome.
Wang X, Cimermancic P, Yu C, Schweitzer A, Chopra N, Engel JL, Greenberg C, Huszagh AS, Beck F, Sakata E, Yang Y, Novitsky EJ, Leitner A, Nanni P, Kahraman A, Guo X, Dixon JE, Rychnovsky SD, Aebersold R, Baumeister W, Sali A, Huang L
Mol Cell Proteomics 16 840-854 (2017)
PMID: 28292943
Related structures: EMD-4089

Function and Biology Details

Reaction catalysed: 
Cleavage of peptide bonds with very broad specificity.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 32-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-126174 (preferred)
Entry contents:
32 distinct polypeptide molecules
Macromolecules (32 distinct):
26S proteasome non-ATPase regulatory subunit 2 Chain: Z
Molecule details ›
Chain: Z
Length: 908 amino acids
Theoretical weight: 100.31 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q13200 (Residues: 1-908; Coverage: 100%)
Gene names: PSMD2, TRAP2
Sequence domains:
Proteasome subunit beta type-6 Chain: 1
Molecule details ›
Chain: 1
Length: 239 amino acids
Theoretical weight: 25.38 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P28072 (Residues: 1-239; Coverage: 100%)
Gene names: LMPY, PSMB6, Y
Sequence domains: Proteasome subunit
Proteasome subunit beta type-7 Chain: 2
Molecule details ›
Chain: 2
Length: 277 amino acids
Theoretical weight: 30 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q99436 (Residues: 1-277; Coverage: 100%)
Gene names: PSMB7, Z
Sequence domains:
Proteasome subunit beta type-3 Chain: 3
Molecule details ›
Chain: 3
Length: 205 amino acids
Theoretical weight: 22.97 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P49720 (Residues: 1-205; Coverage: 100%)
Gene name: PSMB3
Sequence domains: Proteasome subunit
Proteasome subunit beta type-2 Chain: 4
Molecule details ›
Chain: 4
Length: 201 amino acids
Theoretical weight: 22.86 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P49721 (Residues: 1-201; Coverage: 100%)
Gene name: PSMB2
Sequence domains: Proteasome subunit
Proteasome subunit beta type-5 Chain: 5
Molecule details ›
Chain: 5
Length: 263 amino acids
Theoretical weight: 28.51 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P28074 (Residues: 1-263; Coverage: 100%)
Gene names: LMPX, MB1, PSMB5, X
Sequence domains: Proteasome subunit
Proteasome subunit beta type-1 Chain: 6
Molecule details ›
Chain: 6
Length: 241 amino acids
Theoretical weight: 26.52 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P20618 (Residues: 1-241; Coverage: 100%)
Gene names: PSC5, PSMB1
Sequence domains: Proteasome subunit
Proteasome subunit beta type-4 Chain: 7
Molecule details ›
Chain: 7
Length: 264 amino acids
Theoretical weight: 29.23 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P28070 (Residues: 1-264; Coverage: 100%)
Gene names: PROS26, PSMB4
Sequence domains: Proteasome subunit
Proteasome subunit alpha type-6 Chain: A
Molecule details ›
Chain: A
Length: 246 amino acids
Theoretical weight: 27.43 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P60900 (Residues: 1-246; Coverage: 100%)
Gene names: PROS27, PSMA6
Sequence domains:
Proteasome subunit alpha type-2 Chain: B
Molecule details ›
Chain: B
Length: 234 amino acids
Theoretical weight: 25.93 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P25787 (Residues: 1-234; Coverage: 100%)
Gene names: HC3, PSC3, PSMA2
Sequence domains:
Proteasome subunit alpha type-4 Chain: C
Molecule details ›
Chain: C
Length: 261 amino acids
Theoretical weight: 29.53 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P25789 (Residues: 1-261; Coverage: 100%)
Gene names: HC9, PSC9, PSMA4
Sequence domains:
Proteasome subunit alpha type-7 Chain: D
Molecule details ›
Chain: D
Length: 248 amino acids
Theoretical weight: 27.93 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O14818 (Residues: 1-248; Coverage: 100%)
Gene names: HSPC, PSMA7
Sequence domains:
Proteasome subunit alpha type-5 Chain: E
Molecule details ›
Chain: E
Length: 241 amino acids
Theoretical weight: 26.44 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P28066 (Residues: 1-241; Coverage: 100%)
Gene name: PSMA5
Sequence domains:
Proteasome subunit alpha type-1 Chain: F
Molecule details ›
Chain: F
Length: 263 amino acids
Theoretical weight: 29.6 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P25786 (Residues: 1-263; Coverage: 100%)
Gene names: HC2, NU, PROS30, PSC2, PSMA1
Sequence domains:
Proteasome subunit alpha type-3 Chain: G
Molecule details ›
Chain: G
Length: 255 amino acids
Theoretical weight: 28.47 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P25788 (Residues: 1-255; Coverage: 100%)
Gene names: HC8, PSC8, PSMA3
Sequence domains:
26S proteasome regulatory subunit 7 Chain: H
Molecule details ›
Chain: H
Length: 433 amino acids
Theoretical weight: 48.7 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P35998 (Residues: 1-433; Coverage: 100%)
Gene names: MSS1, PSMC2
Sequence domains:
26S proteasome regulatory subunit 4 Chain: I
Molecule details ›
Chain: I
Length: 440 amino acids
Theoretical weight: 49.26 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62191 (Residues: 1-440; Coverage: 100%)
Gene name: PSMC1
Sequence domains:
26S proteasome regulatory subunit 8 Chain: J
Molecule details ›
Chain: J
Length: 406 amino acids
Theoretical weight: 45.69 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62195 (Residues: 1-406; Coverage: 100%)
Gene names: PSMC5, SUG1
Sequence domains:
26S proteasome regulatory subunit 6B Chain: K
Molecule details ›
Chain: K
Length: 418 amino acids
Theoretical weight: 47.43 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P43686 (Residues: 1-418; Coverage: 100%)
Gene names: MIP224, PSMC4, TBP7
Sequence domains:
26S proteasome regulatory subunit 10B Chain: L
Molecule details ›
Chain: L
Length: 389 amino acids
Theoretical weight: 44.24 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62333 (Residues: 1-389; Coverage: 100%)
Gene names: PSMC6, SUG2
Sequence domains:
26S proteasome regulatory subunit 6A Chain: M
Molecule details ›
Chain: M
Length: 439 amino acids
Theoretical weight: 49.27 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P17980 (Residues: 1-439; Coverage: 100%)
Gene names: PSMC3, TBP1
Sequence domains:
26S proteasome non-ATPase regulatory subunit 1 Chain: N
Molecule details ›
Chain: N
Length: 953 amino acids
Theoretical weight: 105.96 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q99460 (Residues: 1-953; Coverage: 100%)
Gene name: PSMD1
Sequence domains:
26S proteasome non-ATPase regulatory subunit 13 Chain: O
Molecule details ›
Chain: O
Length: 376 amino acids
Theoretical weight: 43 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9UNM6 (Residues: 1-376; Coverage: 100%)
Gene name: PSMD13
Sequence domains: PCI domain
26S proteasome non-ATPase regulatory subunit 12 Chain: P
Molecule details ›
Chain: P
Length: 456 amino acids
Theoretical weight: 52.98 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O00232 (Residues: 1-456; Coverage: 100%)
Gene name: PSMD12
Sequence domains:
26S proteasome non-ATPase regulatory subunit 11 Chain: Q
Molecule details ›
Chain: Q
Length: 422 amino acids
Theoretical weight: 47.53 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O00231 (Residues: 1-422; Coverage: 100%)
Gene name: PSMD11
Sequence domains:
26S proteasome non-ATPase regulatory subunit 6 Chain: R
Molecule details ›
Chain: R
Length: 389 amino acids
Theoretical weight: 45.59 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q15008 (Residues: 1-389; Coverage: 100%)
Gene names: KIAA0107, PFAAP4, PSMD6
Sequence domains:
26S proteasome non-ATPase regulatory subunit 3 Chain: S
Molecule details ›
Chain: S
Length: 534 amino acids
Theoretical weight: 61.07 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O43242 (Residues: 1-534; Coverage: 100%)
Gene name: PSMD3
Sequence domains:
26S proteasome non-ATPase regulatory subunit 8 Chain: T
Molecule details ›
Chain: T
Length: 350 amino acids
Theoretical weight: 39.67 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P48556 (Residues: 1-350; Coverage: 100%)
Gene name: PSMD8
Sequence domains: CSN8/PSMD8/EIF3K family
26S proteasome non-ATPase regulatory subunit 7 Chain: U
Molecule details ›
Chain: U
Length: 324 amino acids
Theoretical weight: 37.09 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P51665 (Residues: 1-324; Coverage: 100%)
Gene names: MOV34L, PSMD7
Sequence domains:
26S proteasome non-ATPase regulatory subunit 14 Chain: V
Molecule details ›
Chain: V
Length: 310 amino acids
Theoretical weight: 34.62 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O00487 (Residues: 1-310; Coverage: 100%)
Gene names: POH1, PSMD14
Sequence domains: JAB1/Mov34/MPN/PAD-1 ubiquitin protease
26S proteasome non-ATPase regulatory subunit 4 Chain: W
Molecule details ›
Chain: W
Length: 377 amino acids
Theoretical weight: 40.78 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P55036 (Residues: 1-377; Coverage: 100%)
Gene names: MCB1, PSMD4
Sequence domains:
26S proteasome complex subunit SEM1 Chain: Y
Molecule details ›
Chain: Y
Length: 70 amino acids
Theoretical weight: 8.28 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P60896 (Residues: 1-70; Coverage: 100%)
Gene names: C7orf76, DSS1, SEM1, SHFDG1, SHFM1
Sequence domains: DSS1/SEM1 family

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 6.8Å
Relevant EMDB volumes: EMD-4089

Quick links

Citations

10 review citations

Chemical cross-linking with mass spectrometry: a tool for systems structural biology.
Chavez et al. (2019)
9 more

4 mentions without citation

Principles for Integrative Structural Biology Studies.
Rout et al. (2019)
3 more