1R4N

APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex with ATP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.251 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

The structure of the APPBP1-UBA3-NEDD8-ATP complex reveals the basis for selective ubiquitin-like protein activation by an E1.

Walden, H., Podgorski, M.S., Huang, D.T., Miller, D.W., Howard, R.J., Minor, D.L., Holton, J.M., Schulman, B.A.

(2003) Mol.Cell 12: 1427-1437

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • E1 enzymes initiate ubiquitin-like protein (ubl) transfer cascades by catalyzing adenylation of the ubl's C terminus. An E1's selectivity for its cognate ubl is essential because the E1 subsequently coordinates the ubl with its correct downstream pat ...

    E1 enzymes initiate ubiquitin-like protein (ubl) transfer cascades by catalyzing adenylation of the ubl's C terminus. An E1's selectivity for its cognate ubl is essential because the E1 subsequently coordinates the ubl with its correct downstream pathway. We report here the structure of the 120 kDa quaternary complex between human APPBP1-UBA3, a heterodimeric E1, its ubl NEDD8, and ATP. The E1 selectively recruits NEDD8 through a bipartite interface, involving a domain common to all ubl activating enzymes including bacterial ancestors, and also eukaryotic E1-specific sequences. By modeling ubiquitin into the NEDD8 binding site and performing mutational analysis, we identify a single conserved arginine in APPBP1-UBA3 that acts as a selectivity gate, preventing misactivation of ubiquitin by NEDD8's E1. NEDD8 residues that interact with E1 correspond to residues in ubiquitin important for binding the proteasome and other ubiquitin-interacting proteins, suggesting that the conjugation and recognition machineries have coevolved for each specific ubl.

    Organizational Affiliation: 

    Departments of Structural Biology and Genetics/Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
amyloid beta precursor protein-binding protein 1
A, C, E, G
529Homo sapiensMutation(s): 0 
Gene Names: NAE1 (APPBP1)
Find proteins for Q13564 (Homo sapiens)
Go to Gene View: NAE1
Go to UniProtKB:  Q13564
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ubiquitin-activating enzyme E1C
B, D, F, H
431Homo sapiensMutation(s): 1 
Gene Names: UBA3 (UBE1C)
EC: 6.2.1.-
Find proteins for Q8TBC4 (Homo sapiens)
Go to Gene View: UBA3
Go to UniProtKB:  Q8TBC4
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-like protein NEDD8
I, J, K, L
76Homo sapiensMutation(s): 0 
Gene Names: NEDD8
Find proteins for Q15843 (Homo sapiens)
Go to Gene View: NEDD8
Go to UniProtKB:  Q15843
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP
Download SDF File 
Download CCD File 
B, D, F, H
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ZN
Query on ZN
Download SDF File 
Download CCD File 
F, H, J
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.251 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 135.000α = 90.00
b = 197.900β = 90.00
c = 211.000γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
CNSrefinement
AMoREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-12-23
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-02-01
    Type: Structure summary