5EDV

Structure of the HOIP-RBR/UbcH5B~ubiquitin transfer complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.48 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.249 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of a HOIP/E2~ubiquitin complex reveals RBR E3 ligase mechanism and regulation.

Lechtenberg, B.C.Rajput, A.Sanishvili, R.Dobaczewska, M.K.Ware, C.F.Mace, P.D.Riedl, S.J.

(2016) Nature 529: 546-550

  • DOI: 10.1038/nature16511

  • PubMed Abstract: 
  • Ubiquitination is a central process affecting all facets of cellular signalling and function. A critical step in ubiquitination is the transfer of ubiquitin from an E2 ubiquitin-conjugating enzyme to a substrate or a growing ubiquitin chain, which is ...

    Ubiquitination is a central process affecting all facets of cellular signalling and function. A critical step in ubiquitination is the transfer of ubiquitin from an E2 ubiquitin-conjugating enzyme to a substrate or a growing ubiquitin chain, which is mediated by E3 ubiquitin ligases. RING-type E3 ligases typically facilitate the transfer of ubiquitin from the E2 directly to the substrate. The RING-between-RING (RBR) family of RING-type E3 ligases, however, breaks this paradigm by forming a covalent intermediate with ubiquitin similarly to HECT-type E3 ligases. The RBR family includes Parkin and HOIP, the central catalytic factor of the LUBAC (linear ubiquitin chain assembly complex). While structural insights into the RBR E3 ligases Parkin and HHARI in their overall auto-inhibited forms are available, no structures exist of intact fully active RBR E3 ligases or any of their complexes. Thus, the RBR mechanism of action has remained largely unknown. Here we present the first structure, to our knowledge, of the fully active human HOIP RBR in its transfer complex with an E2~ubiquitin conjugate, which elucidates the intricate nature of RBR E3 ligases. The active HOIP RBR adopts a conformation markedly different from that of auto-inhibited RBRs. HOIP RBR binds the E2~ubiquitin conjugate in an elongated fashion, with the E2 and E3 catalytic centres ideally aligned for ubiquitin transfer, which structurally both requires and enables a HECT-like mechanism. In addition, three distinct helix-IBR-fold motifs inherent to RBRs form ubiquitin-binding regions that engage the activated ubiquitin of the E2~ubiquitin conjugate and, surprisingly, an additional regulatory ubiquitin molecule. The features uncovered reveal critical states of the HOIP RBR E3 ligase cycle, and comparison with Parkin and HHARI suggests a general mechanism for RBR E3 ligases.


    Organizational Affiliation

    NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase RNF31
A, B
380Homo sapiensMutation(s): 0 
Gene Names: RNF31 (ZIBRA)
EC: 2.3.2.31
Find proteins for Q96EP0 (Homo sapiens)
Go to Gene View: RNF31
Go to UniProtKB:  Q96EP0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 D2
C, D, I
149Homo sapiensMutation(s): 2 
Gene Names: UBE2D2 (PUBC1, UBC4, UBC5B, UBCH4, UBCH5B)
EC: 2.3.2.23
Find proteins for P62837 (Homo sapiens)
Go to Gene View: UBE2D2
Go to UniProtKB:  P62837
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-B
E, F, G, H
76Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.48 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.249 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 104.820α = 90.00
b = 75.740β = 95.56
c = 120.960γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
Aimlessdata scaling
PHASERphasing
REFMACrefinement
XDSdata scaling
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Alcohol Abuse and AlcoholismUnited StatesR01AA017238
National Institutes of Health/National Cancer InstituteUnited StatesACB-12002
National Institutes of Health/National Institute of General Medical SciencesUnited StatesAGM-12006

Revision History 

  • Version 1.0: 2016-01-20
    Type: Initial release
  • Version 1.1: 2016-02-03
    Type: Derived calculations
  • Version 1.2: 2016-02-10
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence, Database references, Derived calculations, Refinement description