PDBsum entry 5gjq

Hydrolase

PDB id: 5gjq

Contents

Protein chains

202 a.a.

244 a.a.

220 a.a.

233 a.a.

204 a.a.

250 a.a.

199 a.a.

243 a.a.

201 a.a.

234 a.a.

213 a.a.

238 a.a.

216 a.a.

380 a.a.

359 a.a.

358 a.a.

380 a.a.

375 a.a.

376 a.a.

823 a.a.

243 a.a.

372 a.a.

413 a.a.

421 a.a.

376 a.a.

395 a.a.

258 a.a.

283 a.a.

257 a.a.

193 a.a.

59 a.a.

732 a.a.

355 a.a.

76 a.a.

Ligands

ADP ×6

PDB id:

5gjq

Name:

Hydrolase

Title:

Structure of the human 26s proteasome bound to usp14-ubal

Structure:

Proteasome subunit beta type-6. Chain: a, o. Synonym: macropain delta chain,multicatalytic endopeptidase complex delta chain,proteasome delta chain,proteasome subunit y. Proteasome subunit alpha type-6. Chain: b, h. Synonym: 27 kda prosomal protein,p27k,macropain iota chain, multicatalytic endopeptidase complex iota chain,proteasome iota chain.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: usp14, tgt. Expressed in: escherichia coli k-12. Expression_system_taxid: 83333. Gene: ubb. Expressed in: escherichia coli. Expression_system_taxid: 562

Authors:

X.L.Huang,B.Luan,J.P.Wu,Y.G.Shi

Key ref:

X.Huang et al. (2016). An atomic structure of the human 26S proteasome. Nat Struct Biol, 23, 778-785. PubMed id: 27428775 DOI: 10.1038/nsmb.3273

Date:

01-Jul-16 Release date: 17-Aug-16

Protein chains

P28072  (PSB6_HUMAN) -  Proteasome subunit beta type-6 from Homo sapiens

Seq: 239 a.a.

Struc: 202 a.a.

Protein chains

P60900  (PSA6_HUMAN) -  Proteasome subunit alpha type-6 from Homo sapiens

Seq: 246 a.a.

Struc: 244 a.a.

Protein chains

Q99436  (PSB7_HUMAN) -  Proteasome subunit beta type-7 from Homo sapiens

Seq: 277 a.a.

Struc: 220 a.a.

Protein chains

P25787  (PSA2_HUMAN) -  Proteasome subunit alpha type-2 from Homo sapiens

Seq: 234 a.a.

Struc: 233 a.a.

Protein chains

P49720  (PSB3_HUMAN) -  Proteasome subunit beta type-3 from Homo sapiens

Seq: 205 a.a.

Struc: 204 a.a.

Protein chains

P25789  (PSA4_HUMAN) -  Proteasome subunit alpha type-4 from Homo sapiens

Seq: 261 a.a.

Struc: 250 a.a.

Protein chains

P49721  (PSB2_HUMAN) -  Proteasome subunit beta type-2 from Homo sapiens

Seq: 201 a.a.

Struc: 199 a.a.

Protein chains

O14818  (PSA7_HUMAN) -  Proteasome subunit alpha type-7 from Homo sapiens

Seq: 248 a.a.

Struc: 243 a.a.

Protein chains

P28074  (PSB5_HUMAN) -  Proteasome subunit beta type-5 from Homo sapiens

Seq: 263 a.a.

Struc: 201 a.a.

Protein chains

P28066  (PSA5_HUMAN) -  Proteasome subunit alpha type-5 from Homo sapiens

Seq: 241 a.a.

Struc: 234 a.a.

Protein chains

P20618  (PSB1_HUMAN) -  Proteasome subunit beta type-1 from Homo sapiens

Seq: 241 a.a.

Struc: 213 a.a.

Protein chains

P25786  (PSA1_HUMAN) -  Proteasome subunit alpha type-1 from Homo sapiens

Seq: 263 a.a.

Struc: 238 a.a.

Protein chains

P28070  (PSB4_HUMAN) -  Proteasome subunit beta type-4 from Homo sapiens

Seq: 264 a.a.

Struc: 216 a.a.

Protein chain

P35998  (PRS7_HUMAN) -  26S proteasome regulatory subunit 7 from Homo sapiens

Seq: 433 a.a.

Struc: 380 a.a.

Protein chain

P62191  (PRS4_HUMAN) -  26S proteasome regulatory subunit 4 from Homo sapiens

Seq: 440 a.a.

Struc: 359 a.a.

Protein chain

P62195  (PRS8_HUMAN) -  26S proteasome regulatory subunit 8 from Homo sapiens

Seq: 406 a.a.

Struc: 358 a.a.

Protein chain

P43686  (PRS6B_HUMAN) -  26S proteasome regulatory subunit 6B from Homo sapiens

Seq: 418 a.a.

Struc: 380 a.a.

Protein chain

P62333  (PRS10_HUMAN) -  26S proteasome regulatory subunit 10B from Homo sapiens

Seq: 389 a.a.

Struc: 375 a.a.

Protein chain

P17980  (PRS6A_HUMAN) -  26S proteasome regulatory subunit 6A from Homo sapiens

Seq: 439 a.a.

Struc: 376 a.a.

Protein chain

Q99460  (PSMD1_HUMAN) -  26S proteasome non-ATPase regulatory subunit 1 from Homo sapiens

Seq: 953 a.a.

Struc: 823 a.a.

Protein chains

P25788  (PSA3_HUMAN) -  Proteasome subunit alpha type-3 from Homo sapiens

Seq: 255 a.a.

Struc: 243 a.a.

Protein chain

Q9UNM6  (PSD13_HUMAN) -  26S proteasome non-ATPase regulatory subunit 13 from Homo sapiens

Seq: 376 a.a.

Struc: 372 a.a.

Protein chain

O00232  (PSD12_HUMAN) -  26S proteasome non-ATPase regulatory subunit 12 from Homo sapiens

Seq: 456 a.a.

Struc: 413 a.a.

Protein chain

O00231  (PSD11_HUMAN) -  26S proteasome non-ATPase regulatory subunit 11 from Homo sapiens

Seq: 422 a.a.

Struc: 421 a.a.

Protein chain

Q15008  (PSMD6_HUMAN) -  26S proteasome non-ATPase regulatory subunit 6 from Homo sapiens

Seq: 389 a.a.

Struc: 376 a.a.

Protein chain

O43242  (PSMD3_HUMAN) -  26S proteasome non-ATPase regulatory subunit 3 from Homo sapiens

Seq: 534 a.a.

Struc: 395 a.a.

Protein chain

P48556  (PSMD8_HUMAN) -  26S proteasome non-ATPase regulatory subunit 8 from Homo sapiens

Seq: 350 a.a.

Struc: 258 a.a.

Protein chain

P51665  (PSMD7_HUMAN) -  26S proteasome non-ATPase regulatory subunit 7 from Homo sapiens

Seq: 324 a.a.

Struc: 283 a.a.

Protein chain

O00487  (PSDE_HUMAN) -  26S proteasome non-ATPase regulatory subunit 14 from Homo sapiens

Seq: 310 a.a.

Struc: 257 a.a.

Protein chain

P55036  (PSMD4_HUMAN) -  26S proteasome non-ATPase regulatory subunit 4 from Homo sapiens

Seq: 377 a.a.

Struc: 193 a.a.

Protein chain

P60896  (SEM1_HUMAN) -  26S proteasome complex subunit SEM1 from Homo sapiens

Seq: 70 a.a.

Struc: 59 a.a.

Protein chain

Q13200  (PSMD2_HUMAN) -  26S proteasome non-ATPase regulatory subunit 2 from Homo sapiens

Seq: 908 a.a.

Struc: 732 a.a.

Protein chain

P54578  (UBP14_HUMAN) -  Ubiquitin carboxyl-terminal hydrolase 14 from Homo sapiens

Seq: 494 a.a.

Struc: 355 a.a.

Protein chain

P0CG47  (UBB_HUMAN) -  Polyubiquitin-B from Homo sapiens

Seq: 229 a.a.

Struc: 76 a.a.*

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

Enzyme reactions

• Enzyme class 2: Chains a, B, b, C, c, D, d, E, e, F, f, G, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, X: E.C.3.4.25.1 - proteasome endopeptidase complex.
• Reaction: Cleavage at peptide bonds with very broad specificity.
• Enzyme class 3: Chain V: E.C.3.4.19.- - ?????
• Enzyme class 4: Chain x: 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: 10.1038/nsmb.3273

Nat Struct Biol 23:778-785 (2016)

PubMed id: 27428775

An atomic structure of the human 26S proteasome.

X.Huang, B.Luan, J.Wu, Y.Shi.

ABSTRACT

We report the cryo-EM structure of the human 26S proteasome at an average resolution of 3.5 Å, allowing atomic modeling of 28 subunits in the core particle (CP) and 18 subunits in the regulatory particle (RP). The C-terminal residues of Rpt3 and Rpt5 subunits in the RP can be seen inserted into surface pockets formed between adjacent α subunits in the CP. Each of the six Rpt subunits contains a bound nucleotide, and the central gate of the CP α-ring is closed despite RP association. The six pore 1 loops in the Rpt ring are arranged similarly to a spiral staircase along the axial channel of substrate transport, which is constricted by the pore 2 loops. We also determined the cryo-EM structure of the human proteasome bound to the deubiquitinating enzyme USP14 at 4.35-Å resolution. Together, our structures provide a framework for mechanistic understanding of eukaryotic proteasome function.