3DQV

Structural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control of Conjugation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.249 

wwPDB Validation   3D Report Full Report


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Literature

Structural insights into NEDD8 activation of cullin-RING ligases: conformational control of conjugation.

Duda, D.M., Borg, L.A., Scott, D.C., Hunt, H.W., Hammel, M., Schulman, B.A.

(2008) Cell 134: 995-1006

  • DOI: 10.1016/j.cell.2008.07.022
  • Primary Citation of Related Structures:  
    3DPL, 3DQV

  • PubMed Abstract: 

    • Cullin-RING ligases (CRLs) comprise the largest ubiquitin E3 subclass, in which a central cullin subunit links a substrate-binding adaptor with an E2-binding RING. Covalent attachment of the ubiquitin-like protein NEDD8 to a conserved C-terminal doma ...

    Cullin-RING ligases (CRLs) comprise the largest ubiquitin E3 subclass, in which a central cullin subunit links a substrate-binding adaptor with an E2-binding RING. Covalent attachment of the ubiquitin-like protein NEDD8 to a conserved C-terminal domain (ctd) lysine stimulates CRL ubiquitination activity and prevents binding of the inhibitor CAND1. Here we report striking conformational rearrangements in the crystal structure of NEDD8~Cul5(ctd)-Rbx1 and SAXS analysis of NEDD8~Cul1(ctd)-Rbx1 relative to their unmodified counterparts. In NEDD8ylated CRL structures, the cullin WHB and Rbx1 RING subdomains are dramatically reoriented, eliminating a CAND1-binding site and imparting multiple potential catalytic geometries to an associated E2. Biochemical analyses indicate that the structural malleability is important for both CRL NEDD8ylation and subsequent ubiquitination activities. Thus, our results point to a conformational control of CRL activity, with ligation of NEDD8 shifting equilibria to disfavor inactive CAND1-bound closed architectures, and favor dynamic, open forms that promote polyubiquitination.

    Organizational Affiliation: 

    Howard Hughes Medical Institute, St Jude Children's Research Hospital, Memphis, TN 38105, USA.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NEDD8A, B81Homo sapiensMutation(s): 0 
Gene Names: NEDD8
Find proteins for Q15843 (Homo sapiens)
Explore Q15843 
Go to UniProtKB:  Q15843
NIH Common Fund Data Resources
PHAROS  Q15843
GTEx  ENSG00000129559
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cullin-5C, D382Homo sapiensMutation(s): 0 
Gene Names: CUL5, VACM1
Find proteins for Q93034 (Homo sapiens)
Explore Q93034 
Go to UniProtKB:  Q93034
NIH Common Fund Data Resources
PHAROS  Q93034
GTEx  ENSG00000166266
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Rbx1R, Y106Homo sapiensMutation(s): 0 
Gene Names: RBX1, RNF75, ROC1
EC: 2.3.2.27 (UniProt), 2.3.2.32 (UniProt)
Find proteins for P62877 (Homo sapiens)
Explore P62877 
Go to UniProtKB:  P62877
NIH Common Fund Data Resources
PHAROS  P62877
GTEx  ENSG00000100387
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		A,BL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.249 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.315α = 90
b = 122.442β = 90
c = 128.647γ = 90
Software Package:
Software NamePurpose
SOLVEphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance