8ROV | pdb_00008rov

Human dectin-2 with dimerization domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 
    0.284 (Depositor), 0.284 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Interactions that define the arrangement of sugar-binding sites in BDCA-2 and dectin-2 dimers.

Liu, Y.Kim, J.W.Feinberg, H.Cull, N.Weis, W.I.Taylor, M.E.Drickamer, K.

(2024) Glycobiology 34

  • DOI: https://doi.org/10.1093/glycob/cwae082
  • Primary Citation Related Structures: 
    8ROV

  • PubMed Abstract: 

    The sugar-binding receptors dectin-2 and blood dendritic cell antigen 2 (BDCA-2) bind oligosaccharide ligands through extracellular carbohydrate-recognition domains (CRDs) and initiate intracellular signaling through Fc receptor γ adapters (FcRγ). Dectin-2 stimulates macrophages in response to pathogen binding while BDCA-2 modulates cytokine production in plasmacytoid dendritic cells. The oligomeric states of these receptors and the orientations of their CRDs have been investigated by analysis of a naturally occurring disulfide-bonded variant of BDCA-2 and by replacement of transmembrane domains with N-terminal dimerization domains to create extracellular domain dimers of both dectin-2 and BDCA-2. Analysis of these constructs, as well as previously described crystal structures of the CRDs from these proteins and a novel structure of an extended version of the extracellular domain of dectin-2, showed that there is only limited interaction of the CRDs in the dimers, but interactions can be stabilized by the presence of the neck region. The resulting orientation of sugar-binding sites in the dimers would favor crosslinking of multiple dimers by oligosaccharide ligands, causing clustering of FcRγ to initiate signaling.


  • Organizational Affiliation
    • Department of Life Sciences, Imperial College, London SW7 2AZ, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 44.77 kDa 
  • Atom Count: 2,407 
  • Modeled Residue Count: 290 
  • Deposited Residue Count: 386 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
C-type lectin domain family 6 member A
A, B
193Homo sapiensMutation(s): 0 
Gene Names: CLEC6ACLECSF10DECTIN2
UniProt & NIH Common Fund Data Resources
Find proteins for Q6EIG7 (Homo sapiens)
Explore Q6EIG7 
Go to UniProtKB:  Q6EIG7
PHAROS:  Q6EIG7
GTEx:  ENSG00000205846 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6EIG7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MMA
(Subject of Investigation/LOI)

Query on MMA



Download:Ideal Coordinates CCD File
F [auth A],
J [auth B]
methyl alpha-D-mannopyranoside
C7 H14 O6
HOVAGTYPODGVJG-VEIUFWFVSA-N
CA
(Subject of Investigation/LOI)

Query on CA



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
G [auth B],
H [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free:  0.284 (Depositor), 0.284 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.211α = 90
b = 65.03β = 100.61
c = 81.582γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
UK Research and Innovation (UKRI)United KingdomBB/V014137/1

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-16
    Type: Initial release
  • Version 1.1: 2024-12-25
    Changes: Database references