Biological Assembly 1  

Global Symmetry: Dihedral - D7  (3D View)
Global Stoichiometry: Homo 14-mer - A14 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 334.44 kDa 
• Atom Count: 24,261 
• Modelled Residue Count: 3,038 
• Deposited Residue Count: 3,038 
• Unique protein chains: 1

 3FLP

Crystal structure of native heptameric SAP-like pentraxin from Limulus polyphemus

• PDB DOI: 10.2210/pdb3FLP/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Limulus polyphemus
• Mutation(s): No 


• Deposited: 2008-12-19 Released: 2009-01-20 
• Deposition Author(s): Shrive, A.K., Greenhough, T.J., Armstrong, P.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.223 
• R-Value Work: 0.201 
• R-Value Observed: 0.219 

Literature

Crystal structures of Limulus SAP-like pentraxin reveal two molecular aggregations.

Shrive, A.K., Burns, I., Chou, H.T., Stahlberg, H., Armstrong, P.B., Greenhough, T.J.

(2009) J Mol Biol 386: 1240-1254

• PubMed: 19452596 
• DOI: 10.1016/j.jmb.2009.01.008
• Primary Citation of Related Structures:  
  3FLP, 3FLR, 3FLT


• 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 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.

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Related Citations: 

• C-reactive protein and SAP-like pentraxin are both present in Limulus polyphemus haemolymph: Crystal structure of Limulus SAP
  Shrive, A.K., Metcalfe, A.M., Cartwright, J.R., Greenhough, T.J.
  (1999) J Mol Biol 290: 997

• Complete cDNA sequence of SAP-like pentraxin from Limulus polyphemus: Implications for pentraxin evolution
  Tharia, H.A., Shrive, A.K., Mills, J.D., Arme, C., Williams, G.T., Greenhough, T.J.
  (2002) J Mol Biol 316: 583

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Organizational Affiliation: 

Institute of Science and Technology in Medicine, School of Life Sciences, Keele University, Staffordshire ST5 5BG, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SAP-like pentraxin	A, B, C, D, E, F, G, H, I, J, K, L, M, N	217	Limulus polyphemus	Mutation(s): 0
UniProt
Find proteins for Q8WQK3 (Limulus polyphemus) Explore Q8WQK3  Go to UniProtKB:  Q8WQK3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	AA [auth G], BA [auth G], CA [auth H], DA [auth H], EA [auth I], FA [auth I], GA [auth J], HA [auth J], IA [auth K], JA [auth K], KA [auth L], LA [auth L], MA [auth M], NA [auth M], O [auth A], OA [auth N], P [auth A], PA [auth N], Q [auth B], R [auth B], S [auth C], T [auth C], U [auth D], V [auth D], W [auth E], X [auth E], Y [auth F], Z [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.223 
• R-Value Work: 0.201 
• R-Value Observed: 0.219 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.32	α = 90
b = 167.56	β = 92.5
c = 140.87	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
CNS	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-20 
Deposition Author(s): Shrive, A.K., Greenhough, T.J., Armstrong, P.B.

Revision History  

• Version 1.0: 2009-01-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance