2J2P

L-ficolin complexed to N-acetyl-cystein (150mM)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Structural Insights Into the Innate Immune Recognition Specificities of L- and H-Ficolins.

Garlatti, V., Belloy, N., Martin, L., Lacroix, M., Matsushita, M., Endo, Y., Fujita, T., Fontecilla-Camps, J.C., Arlaud, G.J., Thielens, N.M., Gaboriaud, C.

(2007) Embo J. 26: 623

  • DOI: 10.1038/sj.emboj.7601500
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Innate immunity relies critically upon the ability of a few pattern recognition molecules to sense molecular markers on pathogens, but little is known about these interactions at the atomic level. Human L- and H-ficolins are soluble oligomeric defenc ...

    Innate immunity relies critically upon the ability of a few pattern recognition molecules to sense molecular markers on pathogens, but little is known about these interactions at the atomic level. Human L- and H-ficolins are soluble oligomeric defence proteins with lectin-like activity, assembled from collagen fibers prolonged by fibrinogen-like recognition domains. The X-ray structures of their trimeric recognition domains, alone and in complex with various ligands, have been solved to resolutions up to 1.95 and 1.7 A, respectively. Both domains have three-lobed structures with clefts separating the distal parts of the protomers. Ca(2+) ions are found at sites homologous to those described for tachylectin 5A (TL5A), an invertebrate lectin. Outer binding sites (S1) homologous to the GlcNAc-binding pocket of TL5A are present in the ficolins but show different structures and specificities. In L-ficolin, three additional binding sites (S2-S4) surround the cleft. Together, they define an unpredicted continuous recognition surface able to sense various acetylated and neutral carbohydrate markers in the context of extended polysaccharides such as 1,3-beta-D-glucan, as found on microbial or apoptotic surfaces.

    Organizational Affiliation: 

    Laboratoire de Cristallographie et Cristallogénèse des Protéines, Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FICOLIN-2
A, B, C, D, E, F
218Homo sapiensMutation(s): 0 
Gene Names: FCN2 (FCNL)
Find proteins for Q15485 (Homo sapiens)
Go to Gene View: FCN2
Go to UniProtKB:  Q15485
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA
Download SDF File 
Download CCD File 
A, B, C, D, E, F
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BMA
Query on BMA
Download SDF File 
Download CCD File 
C
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
Download CCD File 
B, E
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
SC2
Query on SC2
Download SDF File 
Download CCD File 
A, B, C, D, E, F
N-ACETYL-L-CYSTEINE
(2R)-2-acetamido-3-sulfanyl-propanoic acid
C5 H9 N O3 S
PWKSKIMOESPYIA-BYPYZUCNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.197 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 96.400α = 90.00
b = 96.400β = 90.00
c = 140.290γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-01-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2015-01-21
    Type: Atomic model, Derived calculations, Non-polymer description, Other
  • Version 1.3: 2019-04-03
    Type: Advisory, Data collection, Derived calculations, Other, Source and taxonomy