Database accession: MF7000582
Name: Rabbit calcyclin (apo form)
PDB ID: 2cnp
Experimental method: NMR
Assembly: Homodimer
Source organism: Oryctolagus cuniculus
Primary publication of the structure:
Mäler L, Potts BC, Chazin WJ
High resolution solution structure of apo calcyclin and structural variations in the S100 family of calcium-binding proteins.
(1999) J. Biomol. NMR 13: 233-47
PMID: 10212984
Abstract:
The three-dimensional solution structure of apo rabbit lung calcyclin has been refined to high resolution through the use of heteronuclear NMR spectroscopy and 13C, 15N-enriched protein. Upon completing the assignment of virtually all of the 15N, 13C and 1H NMR resonances, the solution structure was determined from a combination of 2814 NOE-derived distance constraints, and 272 torsion angle constraints derived from scalar couplings. A large number of critical inter-subunit NOEs (386) were identified from 13C-select, 13C-filtered NOESY experiments, providing a highly accurate dimer interface. The combination of distance geometry and restrained molecular dynamics calculations yielded structures with excellent agreement with the experimental data and high precision (rmsd from the mean for the backbone atoms in the eight helices: 0.33 A). Calcyclin exhibits a symmetric dimeric fold of two identical 90 amino acid subunits, characteristic of the S100 subfamily of EF-hand Ca(2+)-binding proteins. The structure reveals a readily identified pair of putative sites for binding of Zn2+. In order to accurately determine the structural features that differentiate the various S100 proteins, distance difference matrices and contact maps were calculated for the NMR structural ensembles of apo calcyclin and rat and bovine S100B. These data show that the most significant variations among the structures are in the positioning of helix III and in loops, the regions with least sequence similarity. Inter-helical angles and distance differences for the proteins show that the positioning of helix III of calcyclin is most similar to that of bovine S100B, but that the helix interfaces are more closely packed in calcyclin than in either S100B structure. Surprisingly large differences were found in the positioning of helix III in the two S100B structures, despite there being only four non-identical residues, suggesting that one or both of the S100B structures requires further refinement.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
calcium ion binding calcium ion binding
calcium-dependent protein binding calcium-dependent protein binding
S100 protein binding S100 protein binding
Biological process: not assigned
Cellular component:
collagen-containing extracellular matrix collagen-containing extracellular matrix
cytoplasmic side of plasma membrane cytoplasmic side of plasma membrane
cytosol cytosol
extracellular space extracellular space
nuclear envelope nuclear envelope
perinuclear region of cytoplasm perinuclear region of cytoplasm
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: A, B
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: Protein S100-A6
Source organism: Oryctolagus cuniculus
Length: 90 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMASPLDQAIGLLIGIFHKYSGKEGDKHTLSKKELKELIQKELTIGSKLQDAEIVKLMDDLDRNKDQEVNFQEYITFLGALAMIYNEALKG
UniProtKB AC: P30801 (positions: 1-90)
Coverage: 100%
Name: Protein S100-A6
Source organism: Oryctolagus cuniculus
Length: 90 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMASPLDQAIGLLIGIFHKYSGKEGDKHTLSKKELKELIQKELTIGSKLQDAEIVKLMDDLDRNKDQEVNFQEYITFLGALAMIYNEALKG
UniProtKB AC: P30801 (positions: 1-90)
Coverage: 100%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: S-100/ICaBP type EF hand dimer
Evidence level: Direct evidence
Evidence coverage: The full structure participates in mutual synergistic folding.
Complex Evidence:
GuHCl-induced denaturation of the S100B protein dimer showed that it follows a two-state unfolding/refolding process (PMID:11888280). Other S100 proteins also showed two-state unfolding, no folded monomers were observed (PMID:18346834, PMID:18706914). The dimer has a globular and compact structure with the four helices in each subunit aligning to form a unicornate-type four-helix bundle (PMID:11790100). The hydrophobic core extends through the dimer interface.
Chain A:
N/A
Chain B:
N/A
Surface and contacts features:
Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap). Download the CIF file (.cif)
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