4P5O

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

  • Classification: LIGASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli, Trichoplusia ni
  • Mutation(s): Yes 

  • Deposited: 2014-03-18 Released: 2014-07-02 
  • Deposition Author(s): Scott, D.C., Schulman, B.A.
  • Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.3 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
  • Primary Citation of Related Structures:  
    4P5O

  • 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. Electronic address: brenda.schulman@stjude.org.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cullin-1AC368Homo sapiensMutation(s): 0 
Gene Names: CUL1
Find proteins for Q13616 (Homo sapiens)
Explore Q13616 
Go to UniProtKB:  Q13616
NIH Common Fund Data Resources
PHAROS  Q13616
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RBX1BD106Homo sapiensMutation(s): 0 
Gene Names: RBX1RNF75ROC1
EC: 6.3.2 (PDB Primary Data), 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
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DCN1-like protein 1EF200Homo sapiensMutation(s): 0 
Gene Names: DCUN1D1DCUN1L1RP42SCCRODCN1
Find proteins for Q96GG9 (Homo sapiens)
Explore Q96GG9 
Go to UniProtKB:  Q96GG9
NIH Common Fund Data Resources
PHAROS  Q96GG9
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NEDD8-conjugating enzyme Ubc12GI189Homo sapiensMutation(s): 2 
Gene Names: UBE2MUBC12
EC: 6.3.2 (PDB Primary Data), 2.3.2.34 (UniProt)
Find proteins for P61081 (Homo sapiens)
Explore P61081 
Go to UniProtKB:  P61081
NIH Common Fund Data Resources
PHAROS  P61081
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
NEDD8HK81Homo 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
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
B, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.230 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.105α = 90
b = 129.606β = 111.79
c = 119.94γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM069530

Revision History 

  • Version 1.0: 2014-07-02
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Author supporting evidence, Derived calculations, Other, Source and taxonomy
  • Version 1.2: 2019-11-20
    Changes: Author supporting evidence
  • Version 1.3: 2020-01-29
    Changes: Advisory, Derived calculations, Refinement description