4M7F

Crystal structure of tetrameric fibrinogen-like recognition domain of FIBCD1 with bound ManNAc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of the Tetrameric Fibrinogen-like Recognition Domain of Fibrinogen C Domain Containing 1 (FIBCD1) Protein.

Shrive, A.K.Moeller, J.B.Burns, I.Paterson, J.M.Shaw, A.J.Schlosser, A.Sorensen, G.L.Greenhough, T.J.Holmskov, U.

(2014) J.Biol.Chem. 289: 2880-2887

  • DOI: 10.1074/jbc.M113.520577
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The high resolution crystal structures of a recombinant fragment of the C-terminal fibrinogen-like recognition domain of FIBCD1, a vertebrate receptor that binds chitin, have been determined. The overall tetrameric structure shows similarity in struc ...

    The high resolution crystal structures of a recombinant fragment of the C-terminal fibrinogen-like recognition domain of FIBCD1, a vertebrate receptor that binds chitin, have been determined. The overall tetrameric structure shows similarity in structure and aggregation to the horseshoe crab innate immune protein tachylectin 5A. The high affinity ligand N-acetylmannosamine (ManNAc) binds in the S1 site, predominantly via the acetyl group with the oxygen and acetamide nitrogen hydrogen-bonded to the protein and the methyl group inserted into a hydrophobic pocket. The binding of the ManNAc pyranose ring differs markedly between the two independent subunits, but in all structures the binding of the N-acetyl group is conserved. In the native structure, a crystal contact results in one of the independent protomers binding the first GlcNAc of the Asn(340) N-linked glycan on the other independent protomer. In the ligand-bound structure this GlcNAc is replaced by the higher affinity ligand ManNAc. In addition, a sulfate ion has been modeled into the electron density at a location similar to the S3 binding site in L-ficolin, whereas in the native structure an acetate ion has been placed in the S1 N-acetyl binding site, and a sulfate ion has been placed adjacent to this site. These ion binding sites are ideally placed to receive the N-acetyl and sulfate groups of sulfated GalNAc residues of glycosaminoglycans such as chondroitin and dermatan sulfate. Together, these structures give insight into important determinants of ligand selectivity, demonstrating versatility in recognition and binding while maintaining conservation in N-acetyl and calcium binding.


    Organizational Affiliation

    From the Research Institute of Science and Technology in Medicine, School of Life Sciences, Keele University, Staffordshire ST5 5BG, United Kingdom and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fibrinogen C domain-containing protein 1
A, B
226Homo sapiensMutation(s): 0 
Gene Names: FIBCD1
Find proteins for Q8N539 (Homo sapiens)
Go to Gene View: FIBCD1
Go to UniProtKB:  Q8N539
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
BM3
Query on BM3

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Download CCD File 
A, B
2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-MANNOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-UOLFYFMNSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.187 
  • Space Group: P 4
Unit Cell:
Length (Å)Angle (°)
a = 119.540α = 90.00
b = 119.540β = 90.00
c = 44.260γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
GDAdata collection
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-11
    Type: Initial release
  • Version 1.1: 2013-12-25
    Type: Database references
  • Version 1.2: 2014-02-19
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description