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Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome

Electron Microscopy
9.3Å resolution
PDB entry 4cr3 coloured by chain, front view.
PDB entry 4cr3 coloured by chain, side view.
PDB entry 4cr3 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Assembly composition:
hetero 33-mer (preferred)
Entry contents: 33 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: 26S proteasome complex
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Multimeric state: hetero 33-mer
Accessible surface area: 436025.77 Å2
Buried surface area: 139163.26 Å2
Dissociation area: 360.2 Å2
Dissociation energy (ΔGdiss): -26 kcal/mol
Dissociation entropy (TΔSdiss): 29.52 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-126890
Complex Portal ID: CPX-2262

Macromolecules

Proteasome subunit beta type-1
Chain: 1
Length: 215 amino acids
Theoretical weight: 23.57 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38624 (Residues: 1-215; Coverage: 100%)
Gene names: J1407, PRE3, YJL001W
Pfam: Proteasome subunit
InterPro:
Proteasome subunit beta type-1 in PDB entry 4cr3, assembly 1, front view.
Proteasome subunit beta type-1 in PDB entry 4cr3, assembly 1, side view.
Proteasome subunit beta type-1 in PDB entry 4cr3, assembly 1, top view.
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Proteasome subunit beta type-2
Chain: 2
Length: 261 amino acids
Theoretical weight: 28.3 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P25043 (Residues: 1-261; Coverage: 100%)
Gene names: PUP1, YOR157C
Pfam:
InterPro:
Proteasome subunit beta type-2 in PDB entry 4cr3, assembly 1, front view.
Proteasome subunit beta type-2 in PDB entry 4cr3, assembly 1, side view.
Proteasome subunit beta type-2 in PDB entry 4cr3, assembly 1, top view.
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Proteasome subunit beta type-3
Chain: 3
Length: 205 amino acids
Theoretical weight: 22.63 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P25451 (Residues: 1-205; Coverage: 100%)
Gene names: PUP3, YER094C
Pfam: Proteasome subunit
InterPro:
Proteasome subunit beta type-3 in PDB entry 4cr3, assembly 1, front view.
Proteasome subunit beta type-3 in PDB entry 4cr3, assembly 1, side view.
Proteasome subunit beta type-3 in PDB entry 4cr3, assembly 1, top view.
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Proteasome subunit beta type-4
Chain: 4
Length: 198 amino acids
Theoretical weight: 22.55 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P22141 (Residues: 1-198; Coverage: 100%)
Gene names: PRE1, YER012W
Pfam: Proteasome subunit
InterPro:
Proteasome subunit beta type-4 in PDB entry 4cr3, assembly 1, front view.
Proteasome subunit beta type-4 in PDB entry 4cr3, assembly 1, side view.
Proteasome subunit beta type-4 in PDB entry 4cr3, assembly 1, top view.
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Proteasome subunit beta type-5
Chain: 5
Length: 287 amino acids
Theoretical weight: 31.7 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P30656 (Residues: 1-287; Coverage: 100%)
Gene names: DOA3, P8283.10, PRE2, PRG1, YPR103W
Pfam: Proteasome subunit
InterPro:
Proteasome subunit beta type-5 in PDB entry 4cr3, assembly 1, front view.
Proteasome subunit beta type-5 in PDB entry 4cr3, assembly 1, side view.
Proteasome subunit beta type-5 in PDB entry 4cr3, assembly 1, top view.
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Proteasome subunit beta type-6
Chain: 6
Length: 241 amino acids
Theoretical weight: 26.91 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P23724 (Residues: 1-241; Coverage: 100%)
Gene names: PRE7, PRS3, PTS1, YBL0407, YBL041W
Pfam: Proteasome subunit
InterPro:
Proteasome subunit beta type-6 in PDB entry 4cr3, assembly 1, front view.
Proteasome subunit beta type-6 in PDB entry 4cr3, assembly 1, side view.
Proteasome subunit beta type-6 in PDB entry 4cr3, assembly 1, top view.
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Proteasome subunit beta type-7
Chain: 7
Length: 266 amino acids
Theoretical weight: 29.47 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P30657 (Residues: 1-266; Coverage: 100%)
Gene names: PRE4, YFR050C
Pfam: Proteasome subunit
InterPro:
Proteasome subunit beta type-7 in PDB entry 4cr3, assembly 1, front view.
Proteasome subunit beta type-7 in PDB entry 4cr3, assembly 1, side view.
Proteasome subunit beta type-7 in PDB entry 4cr3, assembly 1, top view.
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Proteasome subunit alpha type-1
Chain: A
Length: 252 amino acids
Theoretical weight: 28.03 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P21243 (Residues: 1-252; Coverage: 100%)
Gene names: PRC2, PRS2, SCL1, YGL011C
Pfam:
InterPro:
Proteasome subunit alpha type-1 in PDB entry 4cr3, assembly 1, front view.
Proteasome subunit alpha type-1 in PDB entry 4cr3, assembly 1, side view.
Proteasome subunit alpha type-1 in PDB entry 4cr3, assembly 1, top view.
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Proteasome subunit alpha type-2
Chain: B
Length: 250 amino acids
Theoretical weight: 27.19 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P23639 (Residues: 1-250; Coverage: 100%)
Gene names: PRE8, PRS4, YML092C
Pfam:
InterPro:
Proteasome subunit alpha type-2 in PDB entry 4cr3, assembly 1, front view.
Proteasome subunit alpha type-2 in PDB entry 4cr3, assembly 1, side view.
Proteasome subunit alpha type-2 in PDB entry 4cr3, assembly 1, top view.
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Proteasome subunit alpha type-3
Chain: C
Length: 258 amino acids
Theoretical weight: 28.75 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P23638 (Residues: 1-258; Coverage: 100%)
Gene names: PRE9, PRS5, YGR135W
Pfam:
InterPro:
Proteasome subunit alpha type-3 in PDB entry 4cr3, assembly 1, front view.
Proteasome subunit alpha type-3 in PDB entry 4cr3, assembly 1, side view.
Proteasome subunit alpha type-3 in PDB entry 4cr3, assembly 1, top view.
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Proteasome subunit alpha type-4
Chain: D
Length: 254 amino acids
Theoretical weight: 28.48 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40303 (Residues: 1-254; Coverage: 100%)
Gene names: PRE6, YOL038W
Pfam:
InterPro:
Proteasome subunit alpha type-4 in PDB entry 4cr3, assembly 1, front view.
Proteasome subunit alpha type-4 in PDB entry 4cr3, assembly 1, side view.
Proteasome subunit alpha type-4 in PDB entry 4cr3, assembly 1, top view.
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Proteasome subunit alpha type-5
Chain: E
Length: 260 amino acids
Theoretical weight: 28.65 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32379 (Residues: 1-260; Coverage: 100%)
Gene names: DOA5, G9155, PUP2, YGR253C
Pfam:
InterPro:
Proteasome subunit alpha type-5 in PDB entry 4cr3, assembly 1, front view.
Proteasome subunit alpha type-5 in PDB entry 4cr3, assembly 1, side view.
Proteasome subunit alpha type-5 in PDB entry 4cr3, assembly 1, top view.
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Proteasome subunit alpha type-6
Chain: F
Length: 234 amino acids
Theoretical weight: 25.63 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40302 (Residues: 1-234; Coverage: 100%)
Gene names: PRE5, YM9924.06, YMR314W
Pfam:
InterPro:
Proteasome subunit alpha type-6 in PDB entry 4cr3, assembly 1, front view.
Proteasome subunit alpha type-6 in PDB entry 4cr3, assembly 1, side view.
Proteasome subunit alpha type-6 in PDB entry 4cr3, assembly 1, top view.
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Probable proteasome subunit alpha type-7
Chain: G
Length: 288 amino acids
Theoretical weight: 31.58 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P21242 (Residues: 1-288; Coverage: 100%)
Gene names: O6650, PRC1, PRE10, PRS1, YOR362C
Pfam:
InterPro:
Probable proteasome subunit alpha type-7 in PDB entry 4cr3, assembly 1, front view.
Probable proteasome subunit alpha type-7 in PDB entry 4cr3, assembly 1, side view.
Probable proteasome subunit alpha type-7 in PDB entry 4cr3, assembly 1, top view.
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26S proteasome regulatory subunit 7 homolog
Chain: H
Length: 467 amino acids
Theoretical weight: 52.05 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P33299 (Residues: 1-467; Coverage: 100%)
Gene names: CIM5, RPT1, YKL145W, YTA3
Pfam:
InterPro:
26S proteasome regulatory subunit 7 homolog in PDB entry 4cr3, assembly 1, front view.
26S proteasome regulatory subunit 7 homolog in PDB entry 4cr3, assembly 1, side view.
26S proteasome regulatory subunit 7 homolog in PDB entry 4cr3, assembly 1, top view.
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26S proteasome regulatory subunit 4 homolog
Chain: I
Length: 437 amino acids
Theoretical weight: 48.9 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40327 (Residues: 1-437; Coverage: 100%)
Gene names: D2920, RPT2, YDL007W, YHS4, YTA5
Pfam:
InterPro:
26S proteasome regulatory subunit 4 homolog in PDB entry 4cr3, assembly 1, front view.
26S proteasome regulatory subunit 4 homolog in PDB entry 4cr3, assembly 1, side view.
26S proteasome regulatory subunit 4 homolog in PDB entry 4cr3, assembly 1, top view.
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26S proteasome regulatory subunit 8 homolog
Chain: J
Length: 405 amino acids
Theoretical weight: 45.34 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q01939 (Residues: 1-405; Coverage: 100%)
Gene names: CIM3, CRL3, RPT6, SUG1, TBPY, TBY1, YGL048C
Pfam:
InterPro:
26S proteasome regulatory subunit 8 homolog in PDB entry 4cr3, assembly 1, front view.
26S proteasome regulatory subunit 8 homolog in PDB entry 4cr3, assembly 1, side view.
26S proteasome regulatory subunit 8 homolog in PDB entry 4cr3, assembly 1, top view.
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26S proteasome regulatory subunit 6B homolog
Chain: K
Length: 428 amino acids
Theoretical weight: 47.95 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P33298 (Residues: 1-428; Coverage: 100%)
Gene names: D9509.14, RPT3, YDR394W, YNT1, YTA2
Pfam:
InterPro:
26S proteasome regulatory subunit 6B homolog in PDB entry 4cr3, assembly 1, front view.
26S proteasome regulatory subunit 6B homolog in PDB entry 4cr3, assembly 1, side view.
26S proteasome regulatory subunit 6B homolog in PDB entry 4cr3, assembly 1, top view.
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26S proteasome subunit RPT4
Chain: L
Length: 437 amino acids
Theoretical weight: 49.48 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P53549 (Residues: 1-437; Coverage: 100%)
Gene names: CRL13, PCS1, RPT4, SUG2, YOR259C
Pfam:
InterPro:
26S proteasome subunit RPT4 in PDB entry 4cr3, assembly 1, front view.
26S proteasome subunit RPT4 in PDB entry 4cr3, assembly 1, side view.
26S proteasome subunit RPT4 in PDB entry 4cr3, assembly 1, top view.
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26S proteasome regulatory subunit 6A
Chain: M
Length: 434 amino acids
Theoretical weight: 48.32 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P33297 (Residues: 1-434; Coverage: 100%)
Gene names: O3258, RPT5, YOR117W, YOR3258W, YTA1
Pfam:
InterPro:
26S proteasome regulatory subunit 6A in PDB entry 4cr3, assembly 1, front view.
26S proteasome regulatory subunit 6A in PDB entry 4cr3, assembly 1, side view.
26S proteasome regulatory subunit 6A in PDB entry 4cr3, assembly 1, top view.
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26S proteasome regulatory subunit RPN2
Chain: N
Length: 945 amino acids
Theoretical weight: 104.35 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32565 (Residues: 1-945; Coverage: 100%)
Gene names: RPN2, SEN3, YIL075C
Pfam:
InterPro:
26S proteasome regulatory subunit RPN2 in PDB entry 4cr3, assembly 1, front view.
26S proteasome regulatory subunit RPN2 in PDB entry 4cr3, assembly 1, side view.
26S proteasome regulatory subunit RPN2 in PDB entry 4cr3, assembly 1, top view.
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26S proteasome regulatory subunit RPN9
Chain: O
Length: 393 amino acids
Theoretical weight: 45.84 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q04062 (Residues: 1-393; Coverage: 100%)
Gene names: D9461.14, NAS7, RPN9, YDR427W
Pfam:
InterPro:
26S proteasome regulatory subunit RPN9 in PDB entry 4cr3, assembly 1, front view.
26S proteasome regulatory subunit RPN9 in PDB entry 4cr3, assembly 1, side view.
26S proteasome regulatory subunit RPN9 in PDB entry 4cr3, assembly 1, top view.
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26S proteasome regulatory subunit RPN5
Chain: P
Length: 445 amino acids
Theoretical weight: 51.84 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q12250 (Residues: 1-445; Coverage: 100%)
Gene names: D1572, NAS5, RPN5, YDL147W
Pfam:
InterPro:
26S proteasome regulatory subunit RPN5 in PDB entry 4cr3, assembly 1, front view.
26S proteasome regulatory subunit RPN5 in PDB entry 4cr3, assembly 1, side view.
26S proteasome regulatory subunit RPN5 in PDB entry 4cr3, assembly 1, top view.
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26S proteasome regulatory subunit RPN6
Chain: Q
Length: 434 amino acids
Theoretical weight: 49.84 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q12377 (Residues: 1-434; Coverage: 100%)
Gene names: D2381, NAS4, RPN6, YDL097C
Pfam:
InterPro:
26S proteasome regulatory subunit RPN6 in PDB entry 4cr3, assembly 1, front view.
26S proteasome regulatory subunit RPN6 in PDB entry 4cr3, assembly 1, side view.
26S proteasome regulatory subunit RPN6 in PDB entry 4cr3, assembly 1, top view.
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26S proteasome regulatory subunit RPN7
Chain: R
Length: 429 amino acids
Theoretical weight: 49.02 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q06103 (Residues: 1-429; Coverage: 100%)
Gene names: P8283.8, RPN7, YPR108W
Pfam:
InterPro:
26S proteasome regulatory subunit RPN7 in PDB entry 4cr3, assembly 1, front view.
26S proteasome regulatory subunit RPN7 in PDB entry 4cr3, assembly 1, side view.
26S proteasome regulatory subunit RPN7 in PDB entry 4cr3, assembly 1, top view.
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26S proteasome regulatory subunit RPN3
Chain: S
Length: 523 amino acids
Theoretical weight: 60.46 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40016 (Residues: 1-523; Coverage: 100%)
Gene names: RPN3, SUN2, YER021W
Pfam:
InterPro:
26S proteasome regulatory subunit RPN3 in PDB entry 4cr3, assembly 1, front view.
26S proteasome regulatory subunit RPN3 in PDB entry 4cr3, assembly 1, side view.
26S proteasome regulatory subunit RPN3 in PDB entry 4cr3, assembly 1, top view.
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26S proteasome regulatory subunit RPN12
Chain: T
Length: 274 amino acids
Theoretical weight: 31.95 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32496 (Residues: 1-274; Coverage: 100%)
Gene names: NIN1, RPN12, YFR052W
Pfam: CSN8/PSMD8/EIF3K family
InterPro:
26S proteasome regulatory subunit RPN12 in PDB entry 4cr3, assembly 1, front view.
26S proteasome regulatory subunit RPN12 in PDB entry 4cr3, assembly 1, side view.
26S proteasome regulatory subunit RPN12 in PDB entry 4cr3, assembly 1, top view.
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26S proteasome regulatory subunit RPN8
Chain: U
Length: 338 amino acids
Theoretical weight: 38.37 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q08723 (Residues: 1-338; Coverage: 100%)
Gene names: O5360, RPN8, YOR261C
Pfam:
InterPro:
26S proteasome regulatory subunit RPN8 in PDB entry 4cr3, assembly 1, front view.
26S proteasome regulatory subunit RPN8 in PDB entry 4cr3, assembly 1, side view.
26S proteasome regulatory subunit RPN8 in PDB entry 4cr3, assembly 1, top view.
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Ubiquitin carboxyl-terminal hydrolase RPN11
Chain: V
Length: 306 amino acids
Theoretical weight: 34.44 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P43588 (Residues: 1-306; Coverage: 100%)
Gene names: MPR1, RPN11, YFR004W
Pfam: JAB1/Mov34/MPN/PAD-1 ubiquitin protease
InterPro:
Ubiquitin carboxyl-terminal hydrolase RPN11 in PDB entry 4cr3, assembly 1, front view.
Ubiquitin carboxyl-terminal hydrolase RPN11 in PDB entry 4cr3, assembly 1, side view.
Ubiquitin carboxyl-terminal hydrolase RPN11 in PDB entry 4cr3, assembly 1, top view.
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26S proteasome regulatory subunit RPN10
Chain: W
Length: 268 amino acids
Theoretical weight: 29.78 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38886 (Residues: 1-268; Coverage: 100%)
Gene names: MCB1, RPN10, SUN1, YHR200W
Pfam: von Willebrand factor type A domain
InterPro:
26S proteasome regulatory subunit RPN10 in PDB entry 4cr3, assembly 1, front view.
26S proteasome regulatory subunit RPN10 in PDB entry 4cr3, assembly 1, side view.
26S proteasome regulatory subunit RPN10 in PDB entry 4cr3, assembly 1, top view.
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26S proteasome regulatory subunit RPN13
Chain: X
Length: 156 amino acids
Theoretical weight: 17.92 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: O13563 (Residues: 1-156; Coverage: 100%)
Gene names: DAQ1, RPN13, YLR421C
Pfam: Proteasome complex subunit Rpn13, Pru domain
InterPro:
26S proteasome regulatory subunit RPN13 in PDB entry 4cr3, assembly 1, front view.
26S proteasome regulatory subunit RPN13 in PDB entry 4cr3, assembly 1, side view.
26S proteasome regulatory subunit RPN13 in PDB entry 4cr3, assembly 1, top view.
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26S proteasome complex subunit SEM1
Chain: Y
Length: 89 amino acids
Theoretical weight: 10.4 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: O94742 (Residues: 1-89; Coverage: 100%)
Gene names: DSH1, SEM1, YDR363W-A
Pfam: DSS1/SEM1 family
InterPro: DSS1/SEM1
26S proteasome complex subunit SEM1 in PDB entry 4cr3, assembly 1, front view.
26S proteasome complex subunit SEM1 in PDB entry 4cr3, assembly 1, side view.
26S proteasome complex subunit SEM1 in PDB entry 4cr3, assembly 1, top view.
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26S proteasome regulatory subunit RPN1
Chain: Z
Length: 993 amino acids
Theoretical weight: 109.6 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38764 (Residues: 1-993; Coverage: 100%)
Gene names: HRD2, NAS1, RPD1, RPN1, YHR027C
Pfam:
InterPro:
26S proteasome regulatory subunit RPN1 in PDB entry 4cr3, assembly 1, front view.
26S proteasome regulatory subunit RPN1 in PDB entry 4cr3, assembly 1, side view.
26S proteasome regulatory subunit RPN1 in PDB entry 4cr3, assembly 1, top view.
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