2MY1

Solution structure of Bud31p

• PDB DOI: https://doi.org/10.2210/pdb2MY1/pdb
• BMRB: 25439

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


• Deposited: 2015-01-19 Released: 2015-03-11 
• Deposition Author(s): van Roon, A.M., Yang, J., Mathieu, D., Bermel, W., Nagai, K., Neuhaus, D.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 35 
• Selection Criteria: structures with the lowest energy 

Literature

(113) Cd NMR Experiments Reveal an Unusual Metal Cluster in the Solution Structure of the Yeast Splicing Protein Bud31p.

van Roon, A.M., Yang, J.C., Mathieu, D., Bermel, W., Nagai, K., Neuhaus, D.

(2015) Angew Chem Int Ed Engl 54: 4861-4864

• PubMed: 25703931 
• DOI: https://doi.org/10.1002/anie.201412210
• Primary Citation of Related Structures:  
  2MY1


• PubMed Abstract: 
  

  Establishing the binding topology of structural zinc ions in proteins is an essential part of their structure determination by NMR spectroscopy. Using (113)Cd NMR experiments with (113)Cd-substituted samples is a useful approach but has previously been limited mainly to very small protein domains. Here we used (113)Cd NMR spectroscopy during structure determination of Bud31p, a 157-residue yeast protein containing an unusual Zn3Cys9 cluster, demonstrating that recent hardware developments make this approach feasible for significantly larger systems.

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Organizational Affiliation: 

MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH (UK).

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18.75 kDa 
• Atom Count: 1,300 
• Modelled Residue Count: 159 
• Deposited Residue Count: 159 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pre-mRNA-splicing factor BUD31	A	159	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: BUD31, CWC14, YCR063W, YCR63W, YCR903
UniProt
Find proteins for P25337 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25337  Go to UniProtKB:  P25337

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 35 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-11 
Deposition Author(s): van Roon, A.M., Yang, J., Mathieu, D., Bermel, W., Nagai, K., Neuhaus, D.

Revision History  

• Version 1.0: 2015-03-11
  Type: Initial release
  
• Version 1.1: 2015-04-22
  Changes: Database references
• Version 1.2: 2023-06-14
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.3: 2024-05-15
  Changes: Data collection, Database references