PDBsum entry 6r6h

Ligase

PDB id: 6r6h

Contents

Protein chains

419 a.a.

428 a.a.

400 a.a.

405 a.a.

310 a.a.

281 a.a.

172 a.a.

745 a.a.

105 a.a.

99 a.a.

86 a.a.

150 a.a.

206 a.a.

Metals

_ZN

PDB id:

6r6h

Name:

Ligase

Title:

Structural basis of cullin-2 ring e3 ligase regulation by the cop9 signalosome

Structure:

Cop9 signalosome complex subunit 1. Chain: a. Synonym: signalosome subunit 1,g protein pathway suppressor 1,gps-1, jab1-containing signalosome subunit 1,protein mfh. Engineered: yes. Cop9 signalosome complex subunit 2. Chain: b. Synonym: signalosome subunit 2,alien homolog,jab1-containing signalosome subunit 2,thyroid receptor-interacting protein 15,trip-

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: gps1, cops1, csn1. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Expression_system_cell_line: sf9. Gene: cops2, csn2, trip15. Gene: cops3, csn3.

Authors:

E.P.Morris,S.V.Faull,A.M.C.Lau,A.Politis,F.Beuron,N.Cronin

Key ref:

S.V.Faull et al. (2019). Structural basis of Cullin 2 RING E3 ligase regulation by the COP9 signalosome. Nat Commun, 10, 3814. PubMed id: 31444342 DOI: 10.1038/s41467-019-11772-y

Date:

27-Mar-19 Release date: 28-Aug-19

Protein chain

Q13098  (CSN1_HUMAN) -  COP9 signalosome complex subunit 1 from Homo sapiens

Seq: 491 a.a.

Struc: 419 a.a.

Protein chain

P61201  (CSN2_HUMAN) -  COP9 signalosome complex subunit 2 from Homo sapiens

Seq: 443 a.a.

Struc: 428 a.a.

Protein chain

Q9UNS2  (CSN3_HUMAN) -  COP9 signalosome complex subunit 3 from Homo sapiens

Seq: 423 a.a.

Struc: 400 a.a.

Protein chain

Q9BT78  (CSN4_HUMAN) -  COP9 signalosome complex subunit 4 from Homo sapiens

Seq: 406 a.a.

Struc: 405 a.a.

Protein chain

Q92905  (CSN5_HUMAN) -  COP9 signalosome complex subunit 5 from Homo sapiens

Seq: 334 a.a.

Struc: 310 a.a.

Protein chain

Q7L5N1  (CSN6_HUMAN) -  COP9 signalosome complex subunit 6 from Homo sapiens

Seq: 327 a.a.

Struc: 281 a.a.

Protein chain

Q99627  (CSN8_HUMAN) -  COP9 signalosome complex subunit 8 from Homo sapiens

Seq: 209 a.a.

Struc: 172 a.a.

Protein chain

Q13617  (CUL2_HUMAN) -  Cullin-2 from Homo sapiens

Seq: 745 a.a.

Struc: 745 a.a.

Protein chain

Q15370  (ELOB_HUMAN) -  Elongin-B from Homo sapiens

Seq: 118 a.a.

Struc: 105 a.a.*

Protein chain

Q03071  (ELOC_YEAST) -  Elongin-C from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 99 a.a.

Struc: 99 a.a.

Protein chain

P62877  (RBX1_HUMAN) -  E3 ubiquitin-protein ligase RBX1 from Homo sapiens

Seq: 108 a.a.

Struc: 86 a.a.*

Protein chain

P40337  (VHL_HUMAN) -  von Hippel-Lindau disease tumor suppressor from Homo sapiens

Seq: 213 a.a.

Struc: 150 a.a.*

Protein chain

Q9H9Q2  (CSN7B_HUMAN) -  COP9 signalosome complex subunit 7b from Homo sapiens

Seq: 264 a.a.

Struc: 206 a.a.

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chain E: E.C.3.4.-.-
• Enzyme class 3: Chain R: E.C.2.3.2.27 - RING-type E3 ubiquitin transferase.
• Reaction: S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N₆- ubiquitinyl-[acceptor protein]-L-lysine
• Enzyme class 4: Chain R: E.C.2.3.2.32 - cullin-RING-type E3 NEDD8 transferase.
• Reaction: S-[NEDD8-protein]-yl-[E2 NEDD8-conjugating enzyme]-L-cysteine + [cullin]- L-lysine = [E2 NEDD8-conjugating enzyme]-L-cysteine + N₆-[NEDD8- protein]-yl-[cullin]-L-lysine

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/s41467-019-11772-y

Nat Commun 10:3814 (2019)

PubMed id: 31444342

Structural basis of Cullin 2 RING E3 ligase regulation by the COP9 signalosome.

S.V.Faull, A.M.C.Lau, C.Martens, Z.Ahdash, K.Hansen, H.Yebenes, C.Schmidt, F.Beuron, N.B.Cronin, E.P.Morris, A.Politis.

ABSTRACT

Cullin-Ring E3 Ligases (CRLs) regulate a multitude of cellular pathways through specific substrate receptors. The COP9 signalosome (CSN) deactivates CRLs by removing NEDD8 from activated Cullins. Here we present structures of the neddylated and deneddylated CSN-CRL2 complexes by combining single-particle cryo-electron microscopy (cryo-EM) with chemical cross-linking mass spectrometry (XL-MS). These structures suggest a conserved mechanism of CSN activation, consisting of conformational clamping of the CRL2 substrate by CSN2/CSN4, release of the catalytic CSN5/CSN6 heterodimer and finally activation of the CSN5 deneddylation machinery. Using hydrogen-deuterium exchange (HDX)-MS we show that CRL2 activates CSN5/CSN6 in a neddylation-independent manner. The presence of NEDD8 is required to activate the CSN5 active site. Overall, by synergising cryo-EM with MS, we identify sensory regions of the CSN that mediate its stepwise activation and provide a framework for understanding the regulatory mechanism of other Cullin family members.