6HPR

Crystal structure of cIAP1 RING domain bound to UbcH5B-Ub and a non-covalent Ub


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Structural insights into non-covalent ubiquitin activation of the cIAP1-UbcH5B∼ubiquitin complex.

Patel, A.Sibbet, G.J.Huang, D.T.

(2019) J. Biol. Chem. 294: 1240-1249

  • DOI: 10.1074/jbc.RA118.006045

  • PubMed Abstract: 
  • Ubiquitin (Ub)-conjugating enzymes and Ub ligases control protein degradation and regulate many cellular processes in eukaryotes. Cellular inhibitor of apoptosis protein-1 (cIAP1) plays a central role in apoptosis and tumor necrosis factor signaling. ...

    Ubiquitin (Ub)-conjugating enzymes and Ub ligases control protein degradation and regulate many cellular processes in eukaryotes. Cellular inhibitor of apoptosis protein-1 (cIAP1) plays a central role in apoptosis and tumor necrosis factor signaling. It harbors a C-terminal RING domain that homodimerizes to recruit E2∼Ub (where ∼ denotes a thioester bond) complex to catalyze Ub transfer. Noncovalent Ub binding to the backside of the E2 Ub-conjugating enzyme UbcH5 has previously been shown to enhance RING domain activity, but the molecular basis for this enhancement is unclear. To investigate how dimeric cIAP1 RING activates E2∼Ub for Ub transfer and what role noncovalently bound Ub has in Ub transfer, here we determined the crystal structure of the cIAP1 RING dimer bound to both UbcH5B covalently linked to Ub (UbcH5B-Ub) and a noncovalent Ub to 1.7 Å resolution. The structure along with biochemical analyses revealed that the cIAP1 RING domain interacts with UbcH5B-Ub and thereby promotes the formation of a closed UbcH5B-Ub conformation that primes the thioester bond for Ub transfer. We observed that the noncovalent Ub binds to the backside of UbcH5B and abuts UbcH5B's α1β1-loop, which, in turn, stabilizes the closed UbcH5B-Ub conformation. Our results disclose the mechanism by which cIAP1 RING dimer activates UbcH5B∼Ub and indicate that noncovalent Ub binding further stabilizes the cIAP1-UbcH5B∼Ub complex in the active conformation to stimulate Ub transfer.


    Organizational Affiliation

    From the Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, Scotland, United Kingdom and the Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, Scotland, United Kingdom.,From the Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, Scotland, United Kingdom and the Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, Scotland, United Kingdom d.huang@beatson.gla.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Baculoviral IAP repeat-containing protein 2
A
65Homo sapiensMutation(s): 0 
Gene Names: BIRC2 (API1, MIHB, RNF48)
EC: 2.3.2.27
Find proteins for Q13490 (Homo sapiens)
Go to Gene View: BIRC2
Go to UniProtKB:  Q13490
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-B
B, D
81Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 D2
C
147Homo sapiensMutation(s): 0 
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
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.170 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 79.190α = 90.00
b = 53.600β = 107.57
c = 78.540γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
xia2data reduction
xia2data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-09-21 
  • Released Date: 2018-12-12 
  • Deposition Author(s): Patel, A., Huang, D.T.

Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomA23278

Revision History 

  • Version 1.0: 2018-12-12
    Type: Initial release
  • Version 1.1: 2018-12-19
    Type: Data collection, Database references
  • Version 1.2: 2018-12-26
    Type: Data collection, Database references
  • Version 1.3: 2019-03-06
    Type: Data collection, Database references
  • Version 1.4: 2019-05-08
    Type: Advisory, Data collection, Derived calculations
  • Version 1.5: 2019-07-10
    Type: Data collection