3RTR

A RING E3-substrate complex poised for ubiquitin-like protein transfer: structural insights into cullin-RING ligases


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A RING E3-substrate complex poised for ubiquitin-like protein transfer: structural insights into cullin-RING ligases.

Scott, D.C.Duda, D.M.Grace, C.R.Kurinov, I.Kriwacki, R.W.Schulman, B.A.Calabrese, M.F.

(2011) Nat.Struct.Mol.Biol. 18: 947-949

  • DOI: 10.1038/nsmb.2086

  • PubMed Abstract: 
  • How RING E3 ligases mediate E2-to-substrate ubiquitin-like protein (UBL) transfer remains unknown. Here we address how the RING E3 RBX1 positions NEDD8's E2 (UBC12) and substrate (CUL1). We find that existing structures are incompatible with CUL1 NED ...

    How RING E3 ligases mediate E2-to-substrate ubiquitin-like protein (UBL) transfer remains unknown. Here we address how the RING E3 RBX1 positions NEDD8's E2 (UBC12) and substrate (CUL1). We find that existing structures are incompatible with CUL1 NEDD8ylation and report a new conformation of RBX1 that places UBC12 adjacent to CUL1. We propose RING domain rotation as a general mechanism for UBL transfer for the largest family of E3s.


    Organizational Affiliation

    Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA. matthew.calabrese@stjude.org




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cullin-1
A, C, E, G
368Homo sapiensMutation(s): 4 
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, F, H
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 
B, D, F, H
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.238 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 88.475α = 90.00
b = 119.796β = 90.00
c = 231.861γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-07-20
    Type: Initial release
  • Version 1.1: 2011-08-24
    Type: Database references