Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17.00 kDa 
• Atom Count: 1157 
• Residue Count: 146 
• Unique protein chains: 1

2K61

Solution structure of CaM complexed to DAPk peptide

• DOI: 10.2210/pdb2K61/pdb
• BMRB: 7425
• BMRB: 7424
• BMRB: 7423
• BMRB: 15852

• Classification: METAL BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-07-02 Released: 2009-05-05 
• Deposition Author(s): Bertini, I., Luchinat, C., Parigi, G., Yuan, J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 1 
• Conformers Submitted: 1 
• Selection Criteria: structures with the lowest energy 

Literature

Accurate solution structures of proteins from X-ray data and a minimal set of NMR data: calmodulin-peptide complexes as examples.

Bertini, I., Kursula, P., Luchinat, C., Parigi, G., Vahokoski, J., Wilmanns, M., Yuan, J.

(2009) J Am Chem Soc 131: 5134-5144

• PubMed: 19317469 
• DOI: 10.1021/ja8080764
• Structures With Same Primary Citation


• PubMed Abstract: 
  

A strategy for the accurate determination of protein solution structures starting from X-ray data and a minimal set of NMR data is proposed and successfully applied to two complexes of calmodulin (CaM) with target peptides not previously described. Its implementation in the present case is based on the use of lanthanide ions as substitutes for calcium in one of the four calcium binding sites of CaM and the collection of pseudocontact shift (pcs) and residual dipolar coupling (rdc) restraints induced by the paramagnetic metals. Starting from the crystal structures, new structural models are calculated that are in excellent agreement with the paramagnetic restraints and differ significantly from the starting crystal structures. In particular, in both complexes, a change in orientation of the first helix of the N-terminal CaM domain and of the whole C-terminal domain is observed. The simultaneous use of paramagnetic pcs and rdc restraints has the following crucial advantages: (i) it allows one to assess the possible presence of interdomain conformational freedom, which cannot be detected if the rdc values are derived from external orienting media; (ii) in the absence of significant conformational freedom, the global orientation tensor can be independently and precisely determined from pcs values, which are less sensitive than rdc values to the presence of local structural inaccuracies, and therefore (iii) the relative rearrangement of a domain or a secondary structure element with respect to the metal-bearing domain can be detected.

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Organizational Affiliation: 

Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Calmodulin	A	148	Homo sapiens	Mutation(s): 1  Gene Names:  CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII
Find proteins for P0DP23 (Homo sapiens) Go to UniProtKB:  P0DP23
NIH Common Fund Data Resources
PHAROS  P0DP23 GTEx  ENSG00000198668

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TB	A	TERBIUM(III) ION Tb HKCRVXUAKWXBLE-UHFFFAOYSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 1 
• Conformers Submitted: 1 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2K61 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-07-02 
• Released Date: 2009-05-05 
Deposition Author(s): Bertini, I., Luchinat, C., Parigi, G., Yuan, J.

Revision History 

• Version 1.0: 2009-05-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2016-06-08
  Changes: Derived calculations