2J2P

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report



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:  
    2J0H, 2J0G, 2J0Y, 2J1G, 2J2P, 2J3O, 2J3U, 2J3G, 2J3F, 2J64

  • 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 defence pr ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FICOLIN-2 A, B, C, D, E, F218Homo sapiensMutation(s): 0 
Gene Names: FCN2, FCNL
Find proteins for Q15485 (Homo sapiens)
Explore Q15485 
Go to UniProtKB:  Q15485
NIH Common Fund Data Resources
PHAROS:  Q15485
GTEx:  ENSG00000160339
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, H
2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BMA
Query on BMA
Download Ideal Coordinates CCD File 
C
beta-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N		 Ligand Interaction
SC2
Query on SC2
Download Ideal Coordinates CCD File 
A, B, C, D, E, F
N-ACETYL-L-CYSTEINE
C5 H9 N O3 S
PWKSKIMOESPYIA-BYPYZUCNSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
A, B, C, D, E, F
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.201 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.4α = 90
b = 96.4β = 90
c = 140.29γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-01-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2015-01-21
    Changes: Atomic model, Derived calculations, Non-polymer description, Other
  • Version 1.3: 2019-04-03
    Changes: Advisory, Data collection, Derived calculations, Other, Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary