6A73

Complex structure of CSN2 with IP6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

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: 10.1073/pnas.1911998117
  • Primary Citation of Related Structures:  
    6A73

  • 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 ...

    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

    Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Institute of Neuroscience, Southern University of Science and Technology, Shenzhen, 518055 Guangdong, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 2,EndolysinA, B304Homo sapiensEnterobacteria phage RB59
This entity is chimeric
Mutation(s): 2 
Gene Names: COPS2CSN2TRIP15ERB59_126
EC: 3.2.1.17
UniProt & NIH Common Fund Data Resources
Find proteins for P61201 (Homo sapiens)
Explore P61201 
Go to UniProtKB:  P61201
PHAROS:  P61201
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IHP (Subject of Investigation/LOI)
Query on IHP

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment  



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