Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A3B2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 262.75 kDa 
• Atom Count: 19001 
• Residue Count: 2244 
• Unique protein chains: 2

4NNJ

Crystal structure of Uba1 in complex with ubiquitin-AMP and thioesterified ubiquitin

• DOI: 10.2210/pdb4NNJ/pdb

• Classification: PROTEIN BINDING
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-11-18 Released: 2014-05-07 
• Deposition Author(s): Schaefer, A., Schindelin, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.201 
• R-Value Work: 0.164 
• R-Value Observed: 0.164 

Literature

Structure of the ubiquitin-activating enzyme loaded with two ubiquitin molecules.

Schafer, A., Kuhn, M., Schindelin, H.

(2014) Acta Crystallogr D Biol Crystallogr 70: 1311-1320

• PubMed: 24816100 
• DOI: 10.1107/S1399004714002910
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The activation of ubiquitin by the ubiquitin-activating enzyme Uba1 (E1) constitutes the first step in the covalent modification of target proteins with ubiquitin. This activation is a three-step process in which ubiquitin is adenylated at its C-terminal glycine, followed by the covalent attachment of ubiquitin to a catalytic cysteine residue of Uba1 and the subsequent adenylation of a second ubiquitin. Here, a ubiquitin E1 structure loaded with two ubiquitin molecules is presented for the first time. While one ubiquitin is bound in its adenylated form to the active adenylation domain of E1, the second ubiquitin represents the status after transfer and is covalently linked to the active-site cysteine. The covalently linked ubiquitin enables binding of the E2 enzyme without further modification of the ternary Uba1-ubiquitin2 arrangement. This doubly loaded E1 structure constitutes a missing link in the structural analysis of the ubiquitin-transfer cascade.

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Organizational Affiliation: 

Structural Biology, Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Ubiquitin-activating enzyme E1 1	A, C	1040	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: UBA1, YKL210W EC: 6.2.1.45
Find proteins for P22515 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P22515  Go to UniProtKB:  P22515

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Uba1	B, D, E	79	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: SCD2, UBI4, YLL039C
Find proteins for P0CG63 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CG63  Go to UniProtKB:  P0CG63

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	B, D	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
SO4	A, C	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	A, C	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.201 
• R-Value Work: 0.164 
• R-Value Observed: 0.164 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.04	α = 90
b = 195.651	β = 90
c = 230.629	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
EDNA	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-11-18 
• Released Date: 2014-05-07 
Deposition Author(s): Schaefer, A., Schindelin, H.

Revision History 

• Version 1.0: 2014-05-07
  Type: Initial release
  
• Version 1.1: 2014-09-24
  Changes: Database references