4P5O

Structure of an RBX1-UBC12~NEDD8-CUL1-DCN1 complex: a RING-E3-E2~ubiquitin-like protein-substrate intermediate trapped in action


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1071 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of a RING E3 Trapped in Action Reveals Ligation Mechanism for the Ubiquitin-like Protein NEDD8.

Scott, D.C.Sviderskiy, V.O.Monda, J.K.Lydeard, J.R.Cho, S.E.Harper, J.W.Schulman, B.A.

(2014) Cell 157: 1671-1684

  • DOI: 10.1016/j.cell.2014.04.037

  • PubMed Abstract: 
  • Most E3 ligases use a RING domain to activate a thioester-linked E2∼ubiquitin-like protein (UBL) intermediate and promote UBL transfer to a remotely bound target protein. Nonetheless, RING E3 mechanisms matching a specific UBL and acceptor lysine rem ...

    Most E3 ligases use a RING domain to activate a thioester-linked E2∼ubiquitin-like protein (UBL) intermediate and promote UBL transfer to a remotely bound target protein. Nonetheless, RING E3 mechanisms matching a specific UBL and acceptor lysine remain elusive, including for RBX1, which mediates NEDD8 ligation to cullins and >10% of all ubiquitination. We report the structure of a trapped RING E3-E2∼UBL-target intermediate representing RBX1-UBC12∼NEDD8-CUL1-DCN1, which reveals the mechanism of NEDD8 ligation and how a particular UBL and acceptor lysine are matched by a multifunctional RING E3. Numerous mechanisms specify cullin neddylation while preventing noncognate ubiquitin ligation. Notably, E2-E3-target and RING-E2∼UBL modules are not optimized to function independently, but instead require integration by the UBL and target for maximal reactivity. The UBL and target regulate the catalytic machinery by positioning the RING-E2∼UBL catalytic center, licensing the acceptor lysine, and influencing E2 reactivity, thereby driving their specific coupling by a multifunctional RING E3.


    Organizational Affiliation

    Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; 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
Cullin-1
A, C
368Homo sapiensMutation(s): 0 
Gene Names: CUL1
Find proteins for Q13616 (Homo sapiens)
Go to Gene View: CUL1
Go to UniProtKB:  Q13616
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase RBX1
B, D
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
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DCN1-like protein 1
E, F
200Homo sapiensMutation(s): 0 
Gene Names: DCUN1D1 (DCN1, DCUN1L1, RP42, SCCRO)
Find proteins for Q96GG9 (Homo sapiens)
Go to Gene View: DCUN1D1
Go to UniProtKB:  Q96GG9
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
NEDD8-conjugating enzyme Ubc12
I, G
189Homo sapiensMutation(s): 2 
Gene Names: UBE2M (UBC12)
EC: 2.3.2.-
Find proteins for P61081 (Homo sapiens)
Go to Gene View: UBE2M
Go to UniProtKB:  P61081
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
NEDD8
K, H
81Homo sapiensMutation(s): 0 
Gene Names: NEDD8
Find proteins for Q15843 (Homo sapiens)
Go to Gene View: NEDD8
Go to UniProtKB:  Q15843
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
AME
Query on AME
G, I
NON-POLYMERC7 H13 N O3 S

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1071 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.227 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 89.105α = 90.00
b = 129.606β = 111.79
c = 119.940γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical InstituteUnited States--
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM069530

Revision History 

  • Version 1.0: 2014-07-02
    Type: Initial release
  • Version 1.1: 2017-09-06
    Type: Author supporting evidence, Derived calculations, Other, Source and taxonomy