Database accession: MF7000186
Name: S100A16 (apo form)
PDB ID: 2l50
Experimental method: NMR
Assembly: Homodimer
Source organism: Homo sapiens
Primary publication of the structure:
Babini E, Bertini I, Borsi V, Calderone V, Hu X, Luchinat C, Parigi G
Structural characterization of human S100A16, a low-affinity calcium binder.
(2011) J. Biol. Inorg. Chem. 16: 243-56
PMID: 21046186
Abstract:
The homodimeric structure of human S100A16 in the apo state has been obtained both in the solid state and in solution, resulting in good agreement between the structures with the exception of two loop regions. The homodimeric solution structure of human S100A16 was also calculated in the calcium(II)-bound form. Differently from most S100 proteins, the conformational rearrangement upon calcium binding is minor. This characteristic is likely to be related to the weak binding affinity of the protein for the calcium(II) ions. In turn, this is ascribed to the lack of the glutamate residue at the end of the S100-specific N-domain binding site, which in most S100 proteins provides two important side chain oxygen atoms as calcium(II) ligands. Furthermore, the presence of hydrophobic interactions stronger than for other S100 proteins, present in the closed form of S100A16 between the third and fourth helices, likely make the closed structure of the second EF-hand particularly stable, so even upon calcium(II) binding such a conformation is not disrupted.
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
protein homodimerization activity protein homodimerization activity
RNA binding RNA binding
Biological process:
response to calcium ion response to calcium ion
Cellular component:
cytosol cytosol
extracellular exosome extracellular exosome
extracellular space extracellular space
nucleolus nucleolus
nucleus nucleus
perinuclear region of cytoplasm perinuclear region of cytoplasm
plasma membrane plasma membrane
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-A16
Source organism: Homo sapiens
Length: 103 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMSDCYTELEKAVIVLVENFYKYVSKYSLVKNKISKSSFREMLQKELNHMLSDTGNRKAADKLIQNLDANHDGRISFDEYWTLIGGITGPIAKLIHEQEQQSSS
UniProtKB AC: Q96FQ6 (positions: 2-103)
Coverage: 99%
Name: Protein S100-A16
Source organism: Homo sapiens
Length: 103 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMSDCYTELEKAVIVLVENFYKYVSKYSLVKNKISKSSFREMLQKELNHMLSDTGNRKAADKLIQNLDANHDGRISFDEYWTLIGGITGPIAKLIHEQEQQSSS
UniProtKB AC: Q96FQ6 (positions: 2-103)
Coverage: 99%
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)
Download this entry's XML file (.xml)
Download this entry's JSON file (.json)
