6ZQY

Crystal structure of tetrameric fibrinogen-like recognition domain of FIBCD1 with Neu5Ac ligand bound

• PDB DOI: https://doi.org/10.2210/pdb6ZQY/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2020-07-10 Released: 2021-07-21 
• Deposition Author(s): Shrive, A.K., Greenhough, T.J., Williams, H.M.
• Funding Organization(s): Science and Technology Funding Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.196 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 

Starting Model: experimental

Literature

Crystal structures of human immune protein FIBCD1 suggest an extended binding site compatible with recognition of pathogen associated carbohydrate motifs

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

(2023) J Biol Chem 

• DOI: https://doi.org/10.1016/j.jbc.2023.105552

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Biological Assembly 2  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 52.8 kDa 
• Atom Count: 3,958 
• Modelled Residue Count: 438 
• Deposited Residue Count: 452 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibrinogen C domain-containing protein 1	A, B	226	Homo sapiens	Mutation(s): 0  Gene Names: FIBCD1, UNQ701/PRO1346
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N539 (Homo sapiens) Explore Q8N539  Go to UniProtKB:  Q8N539
PHAROS:  Q8N539 GTEx:  ENSG00000130720
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: Q8N539-1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G11971MR GlyCosmos:  G11971MR GlyGen:  G11971MR

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SLB (Subject of Investigation/LOI)	G [auth A]	N-acetyl-beta-neuraminic acid C11 H19 N O9 SQVRNKJHWKZAKO-PFQGKNLYSA-N
SO4	E [auth A], I [auth B], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACY	F [auth A], K [auth B], L [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
CA	D [auth A], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.196 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 
• Space Group: P 4
• Diffraction Data: https://doi.org/10.21252/hx7e-rd04

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.29	α = 90
b = 119.29	β = 90
c = 44.21	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-07-21 
Deposition Author(s): Shrive, A.K., Greenhough, T.J., Williams, H.M.

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Funding Organization	Location	Grant Number
Science and Technology Funding Council	United Kingdom	MX310

Revision History  

• Version 1.0: 2021-07-21
  Type: Initial release
  
• Version 2.0: 2023-12-13
  Changes: Atomic model, Data collection, Database references, Derived calculations
• Version 2.1: 2023-12-27
  Changes: Database references
• Version 2.2: 2024-01-10
  Changes: Database references
• Version 2.3: 2024-01-31
  Changes: Refinement description
• Version 2.4: 2024-10-09
  Changes: Structure summary