Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 29.34 kDa 
• Atom Count: 2114 
• Modelled Residue Count: 252 
• Deposited Residue Count: 258 
• Unique protein chains: 2

1Y8X

Structural basis for recruitment of Ubc12 by an E2-binding domain in NEDD8's E1

• PDB DOI: 10.2210/pdb1Y8X/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-12-13 Released: 2005-02-08 
• Deposition Author(s): Huang, D.T., Paydar, A., Zhuang, M., Waddell, M.B., Holton, J.M., Schulman, B.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.259 
• R-Value Work: 0.242 

Literature

Structural basis for recruitment of Ubc12 by an E2 binding domain in NEDD8's E1.

Huang, D.T., Paydar, A., Zhuang, M., Waddell, M.B., Holton, J.M., Schulman, B.A.

(2005) Mol Cell 17: 341-350

• PubMed: 15694336 
• DOI: 10.1016/j.molcel.2004.12.020
• Primary Citation of Related Structures:  
  1Y8X


• PubMed Abstract: 
  

E2 conjugating enzymes play a central role in ubiquitin and ubiquitin-like protein (ublp) transfer cascades: the E2 accepts the ublp from the E1 enzyme and then the E2 often interacts with an E3 enzyme to promote ublp transfer to the target. We report here the crystal structure of a complex between the C-terminal domain from NEDD8's heterodimeric E1 (APPBP1-UBA3) and the catalytic core domain of NEDD8's E2 (Ubc12). The structure and associated mutational analyses reveal molecular details of Ubc12 recruitment by NEDD8's E1. Interestingly, the E1's Ubc12 binding domain resembles ubiquitin and recruits Ubc12 in a manner mimicking ubiquitin's interactions with ubiquitin binding domains. Structural comparison with E2-E3 complexes indicates that the E1 and E3 binding sites on Ubc12 may overlap and raises the possibility that crosstalk between E1 and E3 interacting with an E2 could influence the specificity and processivity of ublp transfer.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 M	A	160	Homo sapiens	Mutation(s): 2  Gene Names: UBE2M, UBC12 EC: 6.3.2.19 (PDB Primary Data), 2.3.2.34 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P61081 (Homo sapiens) Explore P61081  Go to UniProtKB:  P61081
PHAROS:  P61081

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-activating enzyme E1C	B	98	Homo sapiens	Mutation(s): 2  Gene Names: UBE1C, UBA3 EC: 6.2.1.64
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TBC4 (Homo sapiens) Explore Q8TBC4  Go to UniProtKB:  Q8TBC4
PHAROS:  Q8TBC4

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.259 
• R-Value Work: 0.242 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.606	α = 90
b = 61.518	β = 90
c = 125.938	γ = 90

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-12-13 
• Released Date: 2005-02-08 
Deposition Author(s): Huang, D.T., Paydar, A., Zhuang, M., Waddell, M.B., Holton, J.M., Schulman, B.A.

Revision History  

• Version 1.0: 2005-02-08
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations