4V3L

RNF38-UB-UbcH5B-Ub complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Activation of a Primed Ring E3-E2-Ubiquitin Complex by Non-Covalent Ubiquitin.

Buetow, L.Gabrielsen, M.Anthony, N.G.Dou, H.Patel, A.Aitkenhead, H.Sibbet, G.J.Smith, B.O.Huang, D.T.

(2015) Mol Cell 58: 297

  • DOI: 10.1016/j.molcel.2015.02.017
  • Primary Citation of Related Structures:  
    4V3K, 4V3L

  • PubMed Abstract: 
  • RING ubiquitin ligases (E3) recruit ubiquitin-conjugate enzymes (E2) charged with ubiquitin (Ub) to catalyze ubiquitination. Non-covalent Ub binding to the backside of certain E2s promotes processive polyUb formation, but the mechanism remains elusiv ...

    RING ubiquitin ligases (E3) recruit ubiquitin-conjugate enzymes (E2) charged with ubiquitin (Ub) to catalyze ubiquitination. Non-covalent Ub binding to the backside of certain E2s promotes processive polyUb formation, but the mechanism remains elusive. Here, we show that backside bound Ub (Ub(B)) enhances both RING-independent and RING-dependent UbcH5B-catalyzed donor Ub (Ub(D)) transfer, but with a more prominent effect in RING-dependent transfer. Ub(B) enhances RING E3s' affinities for UbcH5B-Ub, and RING E3-UbcH5B-Ub complex improves Ub(B)'s affinity for UbcH5B. A comparison of the crystal structures of a RING E3, RNF38, bound to UbcH5B-Ub in the absence and presence of Ub(B), together with molecular dynamics simulation and biochemical analyses, suggests Ub(B) restricts the flexibility of UbcH5B's α1 and α1β1 loop. Ub(B) supports E3 function by stabilizing the RING E3-UbcH5B-Ub complex, thereby improving the catalytic efficiency of Ub transfer. Thus, Ub(B) serves as an allosteric activator of RING E3-mediated Ub transfer.


    Organizational Affiliation

    Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK. Electronic address: d.huang@beatson.gla.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UBIQUITIN-CONJUGATING ENZYME E2 D2A146Homo sapiensMutation(s): 1 
Gene Names: UBE2D2PUBC1UBC4UBC5BUBCH4UBCH5B
EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt), 2.3.2.24 (UniProt)
Find proteins for P62837 (Homo sapiens)
Explore P62837 
Go to UniProtKB:  P62837
NIH Common Fund Data Resources
PHAROS  P62837
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
POLYUBIQUITIN-CBD81Homo sapiensMutation(s): 0 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
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PHAROS  P0CG48
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
E3 UBIQUITIN-PROTEIN LIGASE RNF38C79Homo sapiensMutation(s): 0 
Gene Names: RNF38
EC: 6.3.2.19 (PDB Primary Data), 2.3.2.27 (UniProt)
Find proteins for Q9H0F5 (Homo sapiens)
Explore Q9H0F5 
Go to UniProtKB:  Q9H0F5
NIH Common Fund Data Resources
PHAROS  Q9H0F5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.84α = 90
b = 62.84β = 90
c = 191.06γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-04-08
    Type: Initial release
  • Version 1.1: 2015-04-29
    Changes: Database references
  • Version 1.2: 2019-07-31
    Changes: Advisory, Data collection, Derived calculations