6JJJ

Trimeric structure of Kupffer cell C-type lectin receptor Clec4f


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.254 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Trimeric structure of the mouse Kupffer cell C-type lectin receptor Clec4f.

Ouyang, Z.Felix, J.Zhou, J.Pei, Y.Ma, B.Hwang, P.M.Lemieux, M.J.Gutsche, I.Zheng, F.Wen, Y.

(2020) FEBS Lett 594: 189-198

  • DOI: https://doi.org/10.1002/1873-3468.13565
  • Primary Citation of Related Structures:  
    6JJJ

  • PubMed Abstract: 

    The C-type lectin receptor Clec4f has been identified as a specific surface marker for Kupffer cells, although its ortholog is absent in humans and its biological function remains elusive. Here, we report the crystal structure of a truncated mouse trimeric Clec4f. The orientation between the carbohydrate-recognition domain of Clec4f and its neck region differs from other C-type lectins, resulting in an observed distance of 45 Å between the glycan-binding sites within the Clec4f trimer. Interestingly, the trimeric coiled-coil interface within its heptad neck region contains multiple polyglutamine interactions instead of the predominantly hydrophobic leucine zipper found in other C-type lectin receptors. The Clec4f trimeric structure displays unique features regarding its assembly and ligand recognition, shedding light on the evolution and diversity of the C-type lectin family.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education, Health Science Center, Xi'an Jiaotong University, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C-type lectin domain family 4 member F
A, B, C, D, E
A, B, C, D, E, F
160Mus musculusMutation(s): 0 
Gene Names: Clec4fClecsf13Kclr
UniProt
Find proteins for P70194 (Mus musculus)
Explore P70194 
Go to UniProtKB:  P70194
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP70194
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth B]
J [auth B]
K [auth C]
G [auth A],
H [auth A],
I [auth B],
J [auth B],
K [auth C],
L [auth C],
M [auth D],
N [auth D],
O [auth E],
P [auth E],
Q [auth F],
R [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.254 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.15α = 90.01
b = 75.19β = 90.04
c = 61.2γ = 120.06
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChinaNO.31870132 and NO.81741088

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-14
    Type: Initial release
  • Version 1.1: 2020-01-29
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description