2J0G | pdb_00002j0g

L-ficolin complexed to N-acetyl-mannosamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 
    0.248 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2J0G

Ligand Structure Quality Assessment 


This is version 3.0 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: https://doi.org/10.1038/sj.emboj.7601500
  • Primary Citation Related Structures: 
    2J0G, 2J0H, 2J0Y, 2J1G, 2J2P, 2J3F, 2J3G, 2J3O, 2J3U, 2J5Z, 2J60, 2J61, 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 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.

Macromolecule Content 

  • Total Structure Weight: 151.31 kDa 
  • Atom Count: 10,580 
  • Modeled Residue Count: 1,289 
  • Deposited Residue Count: 1,308 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
FICOLIN-2
A, B, C, D, E
A, B, C, D, E, F
218Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15485 (Homo sapiens)
Explore Q15485 
Go to UniProtKB:  Q15485
PHAROS:  Q15485
GTEx:  ENSG00000160339 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15485
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q15485-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
G
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G17392HI
GlyCosmos: G17392HI
GlyGen: G17392HI
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
H
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G47477HI
GlyCosmos: G47477HI
GlyGen: G47477HI

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BM3

Query on BM3



Download:Ideal Coordinates CCD File
J [auth B],
L [auth C],
O [auth E],
Q [auth F]
2-acetamido-2-deoxy-alpha-D-mannopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-UOLFYFMNSA-N
MAN

Query on MAN



Download:Ideal Coordinates CCD File
R [auth F]alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
I [auth A]
K [auth B]
M [auth C]
N [auth D]
P [auth E]
I [auth A],
K [auth B],
M [auth C],
N [auth D],
P [auth E],
S [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free:  0.248 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.94α = 90
b = 96.94β = 90
c = 139.47γ = 120
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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: 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
  • Version 2.1: 2025-04-09
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 3.0: 2025-10-01
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary