4CCG

Structure of an E2-E3 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the Human Fancl Ring-Ube2T Complex Reveals Determinants of Cognate E3-E2 Selection.

Hodson, C.Purkiss, A.Miles, J.A.Walden, H.

(2014) Structure 22: 337

  • DOI: 10.1016/j.str.2013.12.004
  • Primary Citation of Related Structures:  
    4CCG

  • PubMed Abstract: 
  • The combination of an E2 ubiquitin-conjugating enzyme with an E3 ubiquitin-ligase is essential for ubiquitin modification of a substrate. Moreover, the pairing dictates both the substrate choice and the modification type. The molecular details of generic E3-E2 interactions are well established ...

    The combination of an E2 ubiquitin-conjugating enzyme with an E3 ubiquitin-ligase is essential for ubiquitin modification of a substrate. Moreover, the pairing dictates both the substrate choice and the modification type. The molecular details of generic E3-E2 interactions are well established. Nevertheless, the determinants of selective, specific E3-E2 recognition are not understood. There are ∼40 E2s and ∼600 E3s giving rise to a possible ∼24,000 E3-E2 pairs. Using the Fanconi Anemia pathway exclusive E3-E2 pair, FANCL-Ube2T, we report the atomic structure of the FANCL RING-Ube2T complex, revealing a specific and extensive network of additional electrostatic and hydrophobic interactions. Furthermore, we show that these specific interactions are required for selection of Ube2T over other E2s by FANCL.


    Organizational Affiliation

    Protein Structure and Function Laboratory, Lincoln's Inn Fields Laboratories of the London Research Institute, Cancer Research UK, 44 Lincoln's Inn Fields, London WC2A 3LY, UK; MRC-Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, Dow Street, Dundee DD1 5EH, UK. Electronic address: h.walden@dundee.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UBIQUITIN-CONJUGATING ENZYME E2 TA, B212Homo sapiensMutation(s): 0 
Gene Names: UBE2THSPC150PIG50
EC: 2.3.2.23
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NPD8 (Homo sapiens)
Explore Q9NPD8 
Go to UniProtKB:  Q9NPD8
PHAROS:  Q9NPD8
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
E3 UBIQUITIN-PROTEIN LIGASE FANCLC [auth X], D [auth Y]88Homo sapiensMutation(s): 0 
Gene Names: FANCLPHF9
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NW38 (Homo sapiens)
Explore Q9NW38 
Go to UniProtKB:  Q9NW38
PHAROS:  Q9NW38
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download Ideal Coordinates CCD File 
E [auth A], F [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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I [auth A], S [auth Y]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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G [auth A], H [auth A], K [auth B], O [auth X]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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M [auth X], N [auth X], Q [auth Y], R [auth Y]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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J [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

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L [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
NH4
Query on NH4

Download Ideal Coordinates CCD File 
P [auth X]AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.224α = 90
b = 109.224β = 90
c = 117.728γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-08
    Type: Initial release
  • Version 1.1: 2014-01-15
    Changes: Database references
  • Version 1.2: 2014-02-19
    Changes: Database references