Database accession: MF7000597
Name: S100A5 with Ca2+
PDB ID: 2kax
Experimental method: NMR
Assembly: Homodimer
Source organism: Homo sapiens
Primary publication of the structure:
Bertini I, Das Gupta S, Hu X, Karavelas T, Luchinat C, Parigi G, Yuan J
Solution structure and dynamics of S100A5 in the apo and Ca2+-bound states.
(2009) J. Biol. Inorg. Chem. 14: 1097-107
PMID: 19536568
Abstract:
S100A5 is a calcium binding protein of the S100 family, with one canonical and one S100-specific EF-hand motif per subunit. Although its function is still unknown, it has recently been reported to be one of the S100 proteins able to interact with the receptor for advanced glycation end products. The homodimeric solution structures of S100A5 in both the apo and the calcium(II)-loaded forms have been obtained, and show a conformational rearrangement upon calcium binding. This rearrangement involves, in particular, the hinge loop connecting the N-terminal and the C-terminal EF-hand domains, the reorientation of helix III with respect to helix IV, as common to several S100 proteins, and the elongation of helix IV. The details of the structural changes are important because they must be related to the different functions, still largely unknown, of the different members of the S100 family. For the first time for a full-length S100 protein, relaxation measurements were performed on both the apo and the calcium-bound forms. A quite large mobility was observed in the hinge loop, which is not quenched in the calcium form. The structural differences resulting upon calcium binding change the global shape and the distribution of hydrophobic and charged residues of the S100A5 homodimer in a modest but significantly different manner with respect to the closest homologues S100A4 and S100A6.
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
copper ion binding copper ion binding
protein homodimerization activity protein homodimerization activity
zinc ion binding zinc ion binding
Biological process: not assigned
Cellular component:
neuronal cell body neuronal cell body
nucleus nucleus
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-A5
Source organism: Homo sapiens
Length: 92 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMETPLEKALTTMVTTFHKYSGREGSKLTLSRKELKELIKKELCLGEMKESSIDDLMKSLDKNSDQEIDFKEYSVFLTMLCMAYNDFFLEDNK
UniProtKB AC: P33763 (positions: 1-92)
Coverage: 100%
Name: Protein S100-A5
Source organism: Homo sapiens
Length: 92 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMETPLEKALTTMVTTFHKYSGREGSKLTLSRKELKELIKKELCLGEMKESSIDDLMKSLDKNSDQEIDFKEYSVFLTMLCMAYNDFFLEDNK
UniProtKB AC: P33763 (positions: 1-92)
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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