3DQV

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.249 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

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:  

  • 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NEDD8
A, B
81Homo sapiensMutation(s): 0 
Gene Names: NEDD8
Find proteins for Q15843 (Homo sapiens)
Go to Gene View: NEDD8
Go to UniProtKB:  Q15843
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cullin-5
C, D
382Homo sapiensMutation(s): 0 
Gene Names: CUL5 (VACM1)
Find proteins for Q93034 (Homo sapiens)
Go to Gene View: CUL5
Go to UniProtKB:  Q93034
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Rbx1
R, Y
106Homo sapiensMutation(s): 0 
Gene Names: RBX1 (RNF75, ROC1)
EC: 2.3.2.27, 2.3.2.32
Find proteins for P62877 (Homo sapiens)
Go to Gene View: RBX1
Go to UniProtKB:  P62877
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
R, Y
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, R, Y
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.249 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 88.315α = 90.00
b = 122.442β = 90.00
c = 128.647γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
HKL-2000data reduction
HKL-2000data scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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