Database accession: MF7000591
Name: S100A1 with Ca
PDB ID: 1zfs
Experimental method: NMR
Assembly: Homodimer
Source organism: Rattus norvegicus
Primary publication of the structure:
Wright NT, Varney KM, Ellis KC, Markowitz J, Gitti RK, Zimmer DB, Weber DJ
The three-dimensional solution structure of Ca(2+)-bound S100A1 as determined by NMR spectroscopy.
(2005) J. Mol. Biol. 353: 410-26
PMID: 16169012
Abstract:
S100A1 is an EF-hand-containing Ca(2+)-binding protein that undergoes a conformational change upon binding calcium as is necessary to interact with protein targets and initiate a biological response. To better understand how calcium influences the structure and function of S100A1, the three-dimensional structure of calcium-bound S100A1 was determined by multidimensional NMR spectroscopy and compared to the previously determined structure of apo. In total, 3354 nuclear Overhauser effect-derived distance constraints, 240 dihedral constraints, 160 hydrogen bond constraints, and 362 residual dipolar coupling restraints derived from a series of two-dimensional, three-dimensional, and four-dimensional NMR experiments were used in its structure determination (>21 constraints per residue). As with other dimeric S100 proteins, S100A1 is a symmetric homodimer with helices 1, 1', 4, and 4' associating into an X-type four-helix bundle at the dimer interface. Within each subunit there are four alpha-helices and a short antiparallel beta-sheet typical of two helix-loop-helix EF-hand calcium-binding domains. The addition of calcium did not change the interhelical angle of helices 1 and 2 in the pseudo EF-hand significantly; however, there was a large reorientation of helix 3 in the typical EF-hand. The large conformational change exposes a hydrophobic cleft, defined by residues in the hinge region, the C terminus, and regions of helix 3, which are important for the interaction between S100A1 and a peptide (TRTK-12) derived from the actin-capping protein CapZ.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
ATPase binding ATPase binding
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
S100 protein binding S100 protein binding
Biological process:
negative regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II
positive regulation of sprouting angiogenesis positive regulation of sprouting angiogenesis
regulation of heart contraction regulation of heart contraction
Cellular component:
A band A band
cytoplasm cytoplasm
I band I band
M band M band
mitochondrion mitochondrion
nucleus nucleus
sarcoplasmic reticulum sarcoplasmic reticulum
Z disc Z disc
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-A1
Source organism: Rattus norvegicus
Length: 94 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMGSELETAMETLINVFHAHSGKEGDKYKLSKKELKDLLQTELSSFLDVQKDADAVDKIMKELDENGDGEVDFQEFVVLVAALTVACNNFFWENS
UniProtKB AC: P35467 (positions: 2-94)
Coverage: 98%
Name: Protein S100-A1
Source organism: Rattus norvegicus
Length: 94 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMGSELETAMETLINVFHAHSGKEGDKYKLSKKELKDLLQTELSSFLDVQKDADAVDKIMKELDENGDGEVDFQEFVVLVAALTVACNNFFWENS
UniProtKB AC: P35467 (positions: 2-94)
Coverage: 98%
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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