Database accession: MF7000600
Name: S100B with Ca and Zn
PDB ID: 3d0y
Experimental method: X-ray (1.50 Å)
Assembly: Homodimer
Source organism: Homo sapiens
Primary publication of the structure:
Ostendorp T, Diez J, Heizmann CW, Fritz G
The crystal structures of human S100B in the zinc- and calcium-loaded state at three pH values reveal zinc ligand swapping.
(2011) Biochim. Biophys. Acta 1813: 1083-91
PMID: 20950652
Abstract:
S100B is a homodimeric zinc-, copper-, and calcium-binding protein of the family of EF-hand S100 proteins. Zn(2+) binding to S100B increases its affinity towards Ca(2+) as well as towards target peptides and proteins. Cu(2+) and Zn(2+) bind presumably to the same site in S100B. We determined the structures of human Zn(2+)- and Ca(2+)-loaded S100B at pH 6.5, pH 9, and pH 10 by X-ray crystallography at 1.5, 1.4, and 1.65Å resolution, respectively. Two Zn(2+) ions are coordinated tetrahedrally at the dimer interface by His and Glu residues from both subunits. The crystal structures revealed that ligand swapping occurs for one of the four ligands in the Zn(2+)-binding sites. Whereas at pH 9, the Zn(2+) ions are coordinated by His15, His25, His 85', and His 90', at pH 6.5 and pH 10, His90' is replaced by Glu89'. The results document that the Zn(2+)-binding sites are flexible to accommodate other metal ions such as Cu(2+). Moreover, we characterized the structural changes upon Zn(2+) binding, which might lead to increased affinity towards Ca(2+) as well as towards target proteins. We observed that in Zn(2+)-Ca(2+)-loaded S100B the C-termini of helix IV adopt a distinct conformation. Zn(2+) binding induces a repositioning of residues Phe87 and Phe88, which are involved in target protein binding. This article is part of a Special Issue entitled: 11th European Symposium on Calcium.
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
identical protein binding identical protein binding
protein homodimerization activity protein homodimerization activity
RAGE receptor binding RAGE receptor binding
S100 protein binding S100 protein binding
tau protein binding tau protein binding
zinc ion binding zinc ion binding
Biological process:
adaptive thermogenesis adaptive thermogenesis
axonogenesis axonogenesis
cell adhesion cell adhesion
central nervous system development central nervous system development
learning or memory learning or memory
memory memory
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 neuron differentiation positive regulation of neuron differentiation
regulation of neuronal synaptic plasticity regulation of neuronal synaptic plasticity
sympathetic neuron projection extension sympathetic neuron projection extension
Cellular component:
cytoplasm cytoplasm
cytosol cytosol
extracellular region extracellular region
extracellular space extracellular space
intracellular membrane-bounded organelle intracellular membrane-bounded organelle
neuronal cell body neuronal cell body
nucleoplasm nucleoplasm
nucleus nucleus
perinuclear region of cytoplasm perinuclear region of cytoplasm
ruffle ruffle
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-B
Source organism: Homo sapiens
Length: 92 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMSELEKAMVALIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETLDNDGDGECDFQEFMAFVAMVTTACHEFFEHE
UniProtKB AC: P04271 (positions: 1-90)
Coverage: 97%
Name: Protein S100-B
Source organism: Homo sapiens
Length: 92 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMSELEKAMVALIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETLDNDGDGECDFQEFMAFVAMVTTACHEFFEHE
UniProtKB AC: P04271 (positions: 1-90)
Coverage: 97%
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)
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