Complex structure of CSN2 with IP6

Experimental Data Snapshot

  • Resolution: 2.45 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 

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Basis for metabolite-dependent Cullin-RING ligase deneddylation by the COP9 signalosome.

Lin, H.Zhang, X.Liu, L.Fu, Q.Zang, C.Ding, Y.Su, Y.Xu, Z.He, S.Yang, X.Wei, X.Mao, H.Cui, Y.Wei, Y.Zhou, C.Du, L.Huang, N.Zheng, N.Wang, T.Rao, F.

(2020) Proc Natl Acad Sci U S A 117: 4117-4124

  • DOI: https://doi.org/10.1073/pnas.1911998117
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The Cullin-RING ligases (CRLs) are the largest family of ubiquitin E3s activated by neddylation and regulated by the deneddylase COP9 signalosome (CSN). The inositol polyphosphate metabolites promote the formation of CRL-CSN complexes, but with unclear mechanism of action. Here, we provide structural and genetic evidence supporting inositol hexakisphosphate (IP 6 ) as a general CSN cofactor recruiting CRLs. We determined the crystal structure of IP 6 in complex with CSN subunit 2 (CSN2), based on which we identified the IP 6 -corresponding electron density in the cryoelectron microscopy map of a CRL4A-CSN complex. IP 6 binds to a cognate pocket formed by conserved lysine residues from CSN2 and Rbx1/Roc1, thereby strengthening CRL-CSN interactions to dislodge the E2 CDC34/UBE2R from CRL and to promote CRL deneddylation. IP 6 binding-deficient Csn2 K70E/K70E knockin mice are embryonic lethal. The same mutation disabled Schizosaccharomyces pombe Csn2 from rescuing UV-hypersensitivity of csn2 -null yeast. These data suggest that CRL transition from the E2-bound active state to the CSN-bound sequestered state is critically assisted by an interfacial IP 6 small molecule, whose metabolism may be coupled to CRL-CSN complex dynamics.

  • Organizational Affiliation

    Department of Biology, Southern University of Science and Technology, Shenzhen, 518055 Guangdong, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 2,Endolysin
A, B
304Homo sapiensEnterobacteria phage RB59
This entity is chimeric
Mutation(s): 2 
Gene Names: COPS2CSN2TRIP15eRB59_126
UniProt & NIH Common Fund Data Resources
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Find proteins for P61201 (Homo sapiens)
Explore P61201 
Go to UniProtKB:  P61201
PHAROS:  P61201
GTEx:  ENSG00000166200 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP00720P61201
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.45 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.804α = 107.03
b = 70.164β = 103.94
c = 81.35γ = 90.25
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2018YFA0507103

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-03
    Type: Initial release
  • Version 1.1: 2020-02-12
    Changes: Database references
  • Version 1.2: 2020-02-26
    Changes: Database references
  • Version 1.3: 2020-03-11
    Changes: Database references
  • Version 1.4: 2020-10-14
    Changes: Structure summary
  • Version 1.5: 2023-11-22
    Changes: Data collection, Database references, Refinement description