PDBsum entry 4cr4

Hydrolase

PDB id: 4cr4

Contents

Protein chains

205 a.a.

223 a.a.

204 a.a.

198 a.a.

212 a.a.

222 a.a.

233 a.a.

243 a.a.

250 a.a.

245 a.a.

242 a.a.

243 a.a.

233 a.a.

245 a.a.

359 a.a.

362 a.a.

373 a.a.

381 a.a.

361 a.a.

367 a.a.

849 a.a.

387 a.a.

415 a.a.

431 a.a.

400 a.a.

353 a.a.

272 a.a.

255 a.a.

247 a.a.

197 a.a.

127 a.a.

19 a.a.

813 a.a.

PDB id:

4cr4

Name:

Hydrolase

Title:

Deep classification of a large cryo-em dataset defines the conformational landscape of the 26s proteasome

Structure:

Proteasome component pre3. Chain: 1. Synonym: 20s proteasome beta subunit 1, macropain subunit pre3, multicatalytic endopeptidase complex subunit pre3, proteinase ysce subunit pre3. Proteasome component pup1. Chain: 2. Synonym: 20s proteasome beta subunit 2 macropain subunit pup1, multicatalytic endopeptidase complex subunit pup1, proteinase ysce

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Organism_taxid: 4932

Authors:

P.Unverdorben,F.Beck,P.Sledz,A.Schweitzer,G.Pfeifer,J.M.Plitzko, W.Baumeister,F.Foerster

Key ref:

P.Unverdorben et al. (2014). Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome. Proc Natl Acad Sci U S A, 111, 5544-5549. PubMed id: 24706844 DOI: 10.1073/pnas.1403409111

Date:

25-Feb-14 Release date: 02-Apr-14

Supersedes:

4c0v

Protein chain

P38624  (PSB1_YEAST) -  Proteasome subunit beta type-1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 215 a.a.

Struc: 205 a.a.

Protein chain

P25043  (PSB2_YEAST) -  Proteasome subunit beta type-2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 261 a.a.

Struc: 223 a.a.

Protein chain

P25451  (PSB3_YEAST) -  Proteasome subunit beta type-3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 205 a.a.

Struc: 204 a.a.

Protein chain

P22141  (PSB4_YEAST) -  Proteasome subunit beta type-4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 198 a.a.

Struc: 198 a.a.

Protein chain

P30656  (PSB5_YEAST) -  Proteasome subunit beta type-5 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 287 a.a.

Struc: 212 a.a.*

Protein chain

P23724  (PSB6_YEAST) -  Proteasome subunit beta type-6 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 241 a.a.

Struc: 222 a.a.

Protein chain

P30657  (PSB7_YEAST) -  Proteasome subunit beta type-7 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 266 a.a.

Struc: 233 a.a.

Protein chain

P21243  (PSA1_YEAST) -  Proteasome subunit alpha type-1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 252 a.a.

Struc: 243 a.a.

Protein chain

P23639  (PSA2_YEAST) -  Proteasome subunit alpha type-2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 250 a.a.

Struc: 250 a.a.

Protein chain

P23638  (PSA3_YEAST) -  Proteasome subunit alpha type-3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 258 a.a.

Struc: 245 a.a.

Protein chain

P40303  (PSA4_YEAST) -  Proteasome subunit alpha type-4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 254 a.a.

Struc: 242 a.a.

Protein chain

P32379  (PSA5_YEAST) -  Proteasome subunit alpha type-5 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 260 a.a.

Struc: 243 a.a.

Protein chain

P40302  (PSA6_YEAST) -  Proteasome subunit alpha type-6 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 234 a.a.

Struc: 233 a.a.

Protein chain

P21242  (PSA7_YEAST) -  Probable proteasome subunit alpha type-7 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 288 a.a.

Struc: 245 a.a.

Protein chain

P33299  (PRS7_YEAST) -  26S proteasome regulatory subunit 7 homolog from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 467 a.a.

Struc: 359 a.a.

Protein chain

P40327  (PRS4_YEAST) -  26S proteasome regulatory subunit 4 homolog from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 437 a.a.

Struc: 362 a.a.

Protein chain

Q01939  (PRS8_YEAST) -  26S proteasome regulatory subunit 8 homolog from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 405 a.a.

Struc: 373 a.a.

Protein chain

P33298  (PRS6B_YEAST) -  26S proteasome regulatory subunit 6B homolog from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 428 a.a.

Struc: 381 a.a.

Protein chain

P53549  (PRS10_YEAST) -  26S proteasome subunit RPT4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 437 a.a.

Struc: 361 a.a.

Protein chain

P33297  (PRS6A_YEAST) -  26S proteasome regulatory subunit 6A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 434 a.a.

Struc: 367 a.a.

Protein chain

P32565  (RPN2_YEAST) -  26S proteasome regulatory subunit RPN2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 945 a.a.

Struc: 849 a.a.

Protein chain

Q04062  (RPN9_YEAST) -  26S proteasome regulatory subunit RPN9 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 393 a.a.

Struc: 387 a.a.

Protein chain

Q12250  (RPN5_YEAST) -  26S proteasome regulatory subunit RPN5 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 445 a.a.

Struc: 415 a.a.

Protein chain

Q12377  (RPN6_YEAST) -  26S proteasome regulatory subunit RPN6 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 434 a.a.

Struc: 431 a.a.

Protein chain

Q06103  (RPN7_YEAST) -  26S proteasome regulatory subunit RPN7 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 429 a.a.

Struc: 400 a.a.

Protein chain

P40016  (RPN3_YEAST) -  26S proteasome regulatory subunit RPN3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 523 a.a.

Struc: 353 a.a.

Protein chain

P32496  (RPN12_YEAST) -  26S proteasome regulatory subunit RPN12 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 274 a.a.

Struc: 272 a.a.

Protein chain

Q08723  (RPN8_YEAST) -  26S proteasome regulatory subunit RPN8 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 338 a.a.

Struc: 255 a.a.

Protein chain

P43588  (RPN11_YEAST) -  Ubiquitin carboxyl-terminal hydrolase RPN11 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 306 a.a.

Struc: 247 a.a.

Protein chain

P38886  (RPN10_YEAST) -  26S proteasome regulatory subunit RPN10 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 268 a.a.

Struc: 197 a.a.

Protein chain

O13563  (RPN13_YEAST) -  26S proteasome regulatory subunit RPN13 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 156 a.a.

Struc: 127 a.a.

Protein chain

O94742  (SEM1_YEAST) -  26S proteasome complex subunit SEM1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 89 a.a.

Struc: 19 a.a.

Protein chain

P38764  (RPN1_YEAST) -  26S proteasome regulatory subunit RPN1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 993 a.a.

Struc: 813 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class 1: Chains 1, 2, 3, 4, 5, 6, 7, A, B, C, D, E, F, G: E.C.3.4.25.1 - proteasome endopeptidase complex.
• Reaction: Cleavage at peptide bonds with very broad specificity.
• Enzyme class 2: Chain V: E.C.3.4.19.12 - ubiquitinyl hydrolase 1.
• Reaction: Thiol-dependent hydrolysis of ester, thiolester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

DOI no: 10.1073/pnas.1403409111

Proc Natl Acad Sci U S A 111:5544-5549 (2014)

PubMed id: 24706844

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

P.Unverdorben, F.Beck, P.Śledź, A.Schweitzer, G.Pfeifer, J.M.Plitzko, W.Baumeister, F.Förster.

ABSTRACT

The 26S proteasome is a 2.5 MDa molecular machine that executes the degradation of substrates of the ubiquitin-proteasome pathway. The molecular architecture of the 26S proteasome was recently established by cryo-EM approaches. For a detailed understanding of the sequence of events from the initial binding of polyubiquitylated substrates to the translocation into the proteolytic core complex, it is necessary to move beyond static structures and characterize the conformational landscape of the 26S proteasome. To this end we have subjected a large cryo-EM dataset acquired in the presence of ATP and ATP-γS to a deep classification procedure, which deconvolutes coexisting conformational states. Highly variable regions, such as the density assigned to the largest subunit, Rpn1, are now well resolved and rendered interpretable. Our analysis reveals the existence of three major conformations: in addition to the previously described ATP-hydrolyzing (ATPh) and ATP-γS conformations, an intermediate state has been found. Its AAA-ATPase module adopts essentially the same topology that is observed in the ATPh conformation, whereas the lid is more similar to the ATP-γS bound state. Based on the conformational ensemble of the 26S proteasome in solution, we propose a mechanistic model for substrate recognition, commitment, deubiquitylation, and translocation into the core particle.