Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Crystal structures of Limulus SAP-like pentraxin reveal two molecular aggregations.
Journal, issue, pages	J Mol Biol, Vol. 386, Issue 5, Page 1240-1254, Year 2009
Publish date	Mar 13, 2009
Authors	Annette K Shrive / Ian Burns / Hui-Ting Chou / Henning Stahlberg / Peter B Armstrong / Trevor J Greenhough /
PubMed Abstract	The serum-amyloid-P-component-like pentraxin from Limulus polyphemus, a recently discovered pentraxin species and important effector protein of the hemolymph immune system, displays two distinct ...The serum-amyloid-P-component-like pentraxin from Limulus polyphemus, a recently discovered pentraxin species and important effector protein of the hemolymph immune system, displays two distinct doubly stacked cyclic molecular aggregations, heptameric and octameric. The refined three-dimensional structures determined by X-ray crystallography, both based on the same cDNA sequence, show that each aggregate is constructed from a similar dimer of protomers, which is repeated to make up the ring structure. The native octameric form has been refined at a resolution of 3 A, the native heptameric form at 2.3 A, and the phosphoethanolamine (PE)-bound octameric form at 2.7 A. The existence of the hitherto undescribed heptameric form was confirmed by single-particle analysis using cryo-electron microscopy. In the native structures, the calcium-binding site is similar to that in human pentraxins, with two calcium ions bound in each subunit. Upon binding PE, however, each subunit binds a third calcium ion, with all three calcium ions contributing to the binding and orientation of the bound phosphate group within the ligand-binding pocket. While the phosphate is well-defined in the electron density, the ethanolamine group is poorly defined, suggesting structural and binding variabilities of this group. Although sequence homology with human serum amyloid P component is relatively low, structural homology is high, with very similar overall folds and a common affinity for PE. This is due, in part, to a "topological" equivalence of side-chain position. Identical side chains that are important in both function and fold, from different regions of the sequence in human and Limulus structures, occupy similar space within the overall subunit fold. Sequence and structure alignment, based on the refined three-dimensional structures presented here and the known horseshoe crab pentraxin sequences, suggest that adaptation and refinement of C-reactive-protein-mediated immune responses in these ancient creatures lacking antibody-based immunity are based on adaptation by gene duplication.
External links	J Mol Biol / PubMed:19452596
Methods	EM (single particle) / X-ray diffraction
Resolution	2.3 - 14.0 Å
Structure data	EMDB-1598: Cryo-negative staining electron microscopy reveals the structure and oligomeric state of Limulus SAP-like pentraxin Method: EM (single particle) / Resolution: 14.0 Å PDB-3flp: Crystal structure of native heptameric SAP-like pentraxin from Limulus polyphemus Method: X-RAY DIFFRACTION / Resolution: 2.3 Å PDB-3flr: Crystal structure of native octameric SAP-like pentraxin from Limulus polyphemus Method: X-RAY DIFFRACTION / Resolution: 3.0 Å PDB-3flt: Crystal structure of PE-bound octameric SAP-like pentraxin from Limulus polyphemus Method: X-RAY DIFFRACTION / Resolution: 2.7 Å
Chemicals	ChemComp-CA: Unknown entry ChemComp-HOH: WATER / Water ChemComp-OPE: PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER / Phosphorylethanolamine
Source	limulus polyphemus (Atlantic horseshoe crab)
Keywords	SUGAR BINDING PROTEIN / physiological doubly-stacked heptamer / pentraxin fold / cyclic heptamer / invertebrate lectin / PHYSIOLOGICAL DOUBLY-STACKED OCTAMER / CYCLIC OCTAMER