6ZHU

Yeast Uba1 in complex with Ubc3 and ATP

• PDB DOI: https://doi.org/10.2210/pdb6ZHU/pdb

• Classification: LIGASE
• Organism(s): Saccharomyces cerevisiae S288C, Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-06-23 Released: 2022-01-12 
• Deposition Author(s): Misra, M., Schindelin, H.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.18 Å
• R-Value Free: 0.263 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 

Starting Model: experimental

Literature

ATP induced conformational changes facilitate E1-E2 disulfide bridging in the ubiquitin system

Misra, M., Schaefer, A., Kuhn, M., Pluska, L., Tessmer, I., Sommer, T., Schindelin, H.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: native gel electrophoresis

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 596.1 kDa 
• Atom Count: 37,219 
• Modelled Residue Count: 4,681 
• Deposited Residue Count: 5,276 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2-34 kDa	A [auth B], B [auth F], C [auth D], D [auth H]	295	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: CDC34, DNA6, UBC3, YDR054C, D4211, YD9609.08C EC: 2.3.2.23
UniProt
Find proteins for P14682 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P14682  Go to UniProtKB:  P14682

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-activating enzyme E1 1	E [auth A], F [auth E], G [auth C], H [auth G]	1,024	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: UBA1, YKL210W EC: 6.2.1.45
UniProt
Find proteins for P22515 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P22515  Go to UniProtKB:  P22515

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP (Subject of Investigation/LOI)	I [auth A], K [auth E], M [auth C], O [auth G]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG	J [auth A], L [auth E], N [auth C], P [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.18 Å
• R-Value Free: 0.263 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.636	α = 90
b = 152.408	β = 90.448
c = 252.567	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing
PARROT	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-01-12 
Deposition Author(s): Misra, M., Schindelin, H.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SCHI 425-6/1

Revision History  

• Version 1.0: 2022-01-12
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Refinement description