Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 8.63 kDa 
• Atom Count: 600 
• Modelled Residue Count: 77 
• Deposited Residue Count: 77 
• Unique protein chains: 1

1F55

SOLUTION STRUCTURE OF THE CALCIUM BOUND N-TERMINAL DOMAIN OF YEAST CALMODULIN

• PDB DOI: 10.2210/pdb1F55/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-06-13 Released: 2003-07-15 
• Deposition Author(s): Ishida, H., Takahashi, K., Nakashima, K., Kumaki, Y., Nakata, M., Hikichi, K., Yazawa, M.

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 30 
• Selection Criteria: structures with the lowest energy 

Literature

Solution Structures of the N-terminal Domain of Yeast Calmodulin: Ca2+-Dependent Conformational Change and Its Functional Implication

Ishida, H., Takahashi, K., Nakashima, K., Kumaki, Y., Nakata, M., Hikichi, K., Yazawa, M.

(2000) Biochemistry 39: 13660-13668

• PubMed: 11076504 
• DOI: 10.1021/bi000582x
• Primary Citation of Related Structures:  
  1F54, 1F55


• PubMed Abstract: 
  

We have determined solution structures of the N-terminal half domain (N-domain) of yeast calmodulin (YCM0-N, residues 1-77) in the apo and Ca(2+)-saturated forms by NMR spectroscopy. The Ca(2+)-binding sites of YCM0-N consist of a pair of helix-loop-helix motifs (EF-hands), in which the loops are linked by a short beta-sheet. The binding of two Ca(2+) causes large rearrangement of the four alpha-helices and exposes the hydrophobic surface as observed for vertebrate calmodulin (CaM). Within the observed overall conformational similarity in the peptide backbone, several significant conformational differences were observed between the two proteins, which originated from the 38% disagreement in amino acid sequences. The beta-sheet in apo YCM0-N is strongly twisted compared with that in the N-domain of CaM, while it turns to the normal more stable conformation on Ca(2+) binding. YCM0-N shows higher cooperativity in Ca(2+) binding than the N-domain of CaM, and the observed conformational change of the beta-sheet is a possible cause of the highly cooperative Ca(2+) binding. The hydrophobic surface on Ca(2+)-saturated YCM0-N appears less flexible due to the replacements of Met51, Met71, and Val55 in the hydrophobic surface of CaM with Leu51, Leu71, and Ile55, which is thought to be one of reasons for the poor activation of target enzymes by yeast CaM.

---

Organizational Affiliation: 

Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CALMODULIN	A	77	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P06787 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P06787  Go to UniProtKB:  P06787

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 30 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 1F55 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-06-13 
• Released Date: 2003-07-15 
Deposition Author(s): Ishida, H., Takahashi, K., Nakashima, K., Kumaki, Y., Nakata, M., Hikichi, K., Yazawa, M.

Revision History  

• Version 1.0: 2003-07-15
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-16
  Changes: Database references, Derived calculations