Database accession: MF7000584
Name: S100A1 (apo form)
PDB ID: 1k2h
Experimental method: NMR
Assembly: Homodimer
Source organism: Rattus norvegicus
Primary publication of the structure:
Rustandi RR, Baldisseri DM, Inman KG, Nizner P, Hamilton SM, Landar A, Landar A, Zimmer DB, Weber DJ
Three-dimensional solution structure of the calcium-signaling protein apo-S100A1 as determined by NMR.
(2002) Biochemistry 41: 788-96
PMID: 11790100
Abstract:
S100A1, a member of the S100 protein family, is an EF-hand containing Ca(2+)-binding protein (93 residues per subunit) with noncovalent interactions at its dimer interface. Each subunit of S100A1 has four alpha-helices and a small antiparallel beta-sheet consistent with two helix-loop-helix calcium-binding domains [Baldiserri et al. (1999) J. Biomol. NMR 14, 87-88]. In this study, the three-dimensional structure of reduced apo-S100A1 was determined by NMR spectroscopy using a total of 2220 NOE distance constraints, 258 dihedral angle constraints, and 168 backbone hydrogen bond constraints derived from a series of 2D, 3D, and 4D NMR experiments. The final structure was found to be globular and compact with the four helices in each subunit aligning to form a unicornate-type four-helix bundle. Intermolecular NOE correlations were observed between residues in helices 1 and 4 from one subunit to residues in helices 1' and 4' of the other subunit, respectively, consistent with the antiparallel alignment of the two subunits to form a symmetric X-type four-helix bundle as found for other members of the S100 protein family. Because of the similarity of the S100A1 dimer interface to that found for S100B, it was possible to calculate a model of the S100A1/B heterodimer. This model is consistent with a number of NMR chemical shift changes observed when S100A1 is titrated into a sample of (15)N-labeled S100B. Helix 3 (and 3') of S100A1 was found to have an interhelical angle of -150 degrees with helix 4 (and 4') in the apo state. This crossing angle is quite different (>50 degrees ) from that typically found in other EF-hand containing proteins such as apocalmodulin and apotroponin C but more similar to apo-S100B, which has an interhelical angle of -166 degrees. As with S100B, it is likely that the second EF-hand of apo-S100A1 reorients dramatically upon the addition of Ca(2+), which can explain the Ca(2+) dependence that S100A1 has for binding several of its biological targets.
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)
Download this entry's XML file (.xml)
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