Database accession: MF7000594
Name: Human S100A13 with Ca
PDB ID: 2egd
Experimental method: X-ray (1.80 Å)
Assembly: Homodimer
Source organism: Homo sapiens
Primary publication of the structure:
Imai FL, Nagata K, Yonezawa N, Nakano M, Tanokura M
Structure of calcium-bound human S100A13 at pH 7.5 at 1.8 A resolution.
(2008) Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 64: 70-6
PMID: 18259052
Abstract:
S100A13 is a member of the S100 family of EF-hand-containing calcium-binding proteins. S100A13 plays an important role in the secretion of fibroblast growth factor-1 and interleukin 1 alpha, two pro-angiogenic factors released by the nonclassical endoplasmic reticulum/Golgi-independent secretory pathway. The X-ray crystal structure of human S100A13 at pH 7.5 was determined at 1.8 A resolution. The structure was solved by molecular replacement and was refined to a final R factor of 19.0%. The structure revealed that human S100A13 exists as a homodimer with two calcium ions bound to each protomer. The protomer is composed of four alpha-helices (alpha(1)-alpha(4)), which form a pair of EF-hand motifs. Dimerization occurs by hydrophobic interactions between helices alpha(1) and alpha(4) and by intermolecular hydrogen bonds between residues from helix alpha(1) and the residues between alpha(2) and alpha(3) of both chains. Despite the high similarity of the backbone conformation in each protomer, the crystal structures of human S100A13 at pH 7.5 (this study) and at pH 6.0 [Li et al. (2007), Biochem. Biophys. Res. Commun. 356, 616-621] exhibit recognizable differences in the relative orientation ( approximately 2.5 degrees) of the protomers within the dimer and also remarkable differences in the side-chain conformations of several amino-acid residues.
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
fibroblast growth factor binding fibroblast growth factor binding
lipid binding lipid binding
protein homodimerization activity protein homodimerization activity
RAGE receptor binding RAGE receptor binding
zinc ion binding zinc ion binding
Biological process:
mast cell degranulation mast cell degranulation
positive regulation of canonical NF-kappaB signal transduction positive regulation of canonical NF-kappaB signal transduction
positive regulation of cell population proliferation positive regulation of cell population proliferation
positive regulation of cytokine production positive regulation of cytokine production
positive regulation of interleukin-1 alpha production positive regulation of interleukin-1 alpha production
protein transport protein transport
Cellular component:
cytoplasm cytoplasm
cytosol cytosol
extracellular region extracellular region
extracellular space extracellular space
nucleolus nucleolus
nucleoplasm nucleoplasm
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-A13
Source organism: Homo sapiens
Length: 98 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMAAEPLTELEESIETVVTTFFTFARQEGRKDSLSVNEFKELVTQQLPHLLKDVGSLDEKMKSLDVNQDSELKFNEYWRLIGELAKEIRKKKDLKIRKK
UniProtKB AC: Q99584 (positions: 5-90)
Coverage: 87%
Name: Protein S100-A13
Source organism: Homo sapiens
Length: 98 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMAAEPLTELEESIETVVTTFFTFARQEGRKDSLSVNEFKELVTQQLPHLLKDVGSLDEKMKSLDVNQDSELKFNEYWRLIGELAKEIRKKKDLKIRKK
UniProtKB AC: Q99584 (positions: 6-96)
Coverage: 92%
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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