2JHL

Structure of globular heads of M-ficolin complexed with sialic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Basis for Innate Immune Sensing by M-Ficolin and its Control by a Ph-Dependent Conformational Switch.

Garlatti, V.Martin, L.Gout, E.Reiser, J.B.Fujita, T.Arlaud, G.J.Thielens, N.M.Gaboriaud, C.

(2007) J.Biol.Chem. 282: 35814

  • DOI: 10.1074/jbc.M705741200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ficolins are soluble oligomeric proteins with lectin-like activity, assembled from collagen fibers prolonged by fibrinogen-like recognition domains. They act as innate immune sensors by recognizing conserved molecular markers exposed on microbial sur ...

    Ficolins are soluble oligomeric proteins with lectin-like activity, assembled from collagen fibers prolonged by fibrinogen-like recognition domains. They act as innate immune sensors by recognizing conserved molecular markers exposed on microbial surfaces and thereby triggering effector mechanisms such as enhanced phagocytosis and inflammation. In humans, L- and H-ficolins have been characterized in plasma, whereas a third species, M-ficolin, is secreted by monocytes and macrophages. To decipher the molecular mechanisms underlying their recognition properties, we previously solved the structures of the recognition domains of L- and H-ficolins, in complex with various model ligands (Garlatti, V., Belloy, N., Martin, L., Lacroix, M., Matsushita, M., Endo, Y., Fujita, T., Fontecilla-Camps, J. C., Arlaud, G. J., Thielens, N. M., and Gaboriaud, C. (2007) EMBO J. 24, 623-633). We now report the ligand-bound crystal structures of the recognition domain of M-ficolin, determined at high resolution (1.75-1.8 A), which provides the first structural insights into its binding properties. Interaction with acetylated carbohydrates differs from the one previously described for L-ficolin. This study also reveals the structural determinants for binding to sialylated compounds, a property restricted to human M-ficolin and its mouse counterpart, ficolin B. Finally, comparison between the ligand-bound structures obtained at neutral pH and nonbinding conformations observed at pH 5.6 reveals how the ligand binding site is dislocated at acidic pH. This means that the binding function of M-ficolin is subject to a pH-sensitive conformational switch. Considering that the homologous ficolin B is found in the lysosomes of activated macrophages (Runza, V. L., Hehlgans, T., Echtenacher, B., Zahringer, U., Schwaeble, W. J., and Mannel, D. N. (2006) J. Endotoxin Res. 12, 120-126), we propose that this switch could play a physiological role in such acidic compartments.


    Organizational Affiliation

    Laboratoire de Cristallographie et Cristallogénèse des Protéines, Institut de Biologie Structurale Jean-Pierre Ebel, Commissariat à l'Energie Atomique-CNRS-Université Joseph Fourier, 38027 Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FICOLIN-1
F
218Homo sapiensMutation(s): 0 
Gene Names: FCN1 (FCNM)
Find proteins for O00602 (Homo sapiens)
Go to Gene View: FCN1
Go to UniProtKB:  O00602
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
F
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
SLB
Query on SLB

Download SDF File 
Download CCD File 
F
5-N-ACETYL-BETA-D-NEURAMINIC ACID
BETA-SIALIC ACID
C11 H19 N O9
SQVRNKJHWKZAKO-PFQGKNLYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.210 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 72.930α = 90.00
b = 72.930β = 90.00
c = 124.830γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-10-09
    Type: Initial release
  • Version 1.1: 2012-06-13
    Type: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Version format compliance