5H4B

Crystal structure of Cbln4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Cbln1 and Cbln4 Are Structurally Similar but Differ in GluD2 Binding Interactions.

Zhong, C.Shen, J.Zhang, H.Li, G.Shen, S.Wang, F.Hu, K.Cao, L.He, Y.Ding, J.

(2017) Cell Rep 20: 2328-2340

  • DOI: 10.1016/j.celrep.2017.08.031
  • Primary Citation of Related Structures:  
  • Also Cited By: 5H4B

  • PubMed Abstract: 
  • Unlike cerebellin 1 (Cbln1), which bridges neurexin (Nrxn) receptors and δ-type glutamate receptors in a trans-synaptic triad, Cbln4 was reported to have no or weak binding for the receptors despite sharing ∼70% sequence identity with Cbln1. Here, we ...

    Unlike cerebellin 1 (Cbln1), which bridges neurexin (Nrxn) receptors and δ-type glutamate receptors in a trans-synaptic triad, Cbln4 was reported to have no or weak binding for the receptors despite sharing ∼70% sequence identity with Cbln1. Here, we report crystal structures of the homotrimers of the C1q domain of Cbln1 and Cbln4 at 2.2 and 2.3 Å resolution, respectively. Comparison of the structures suggests that the difference between Cbln1 and Cbln4 in GluD2 binding might be because of their sequence and structural divergence in loop CD. Surprisingly, we show that Cbln4 binds to Nrxn1β and forms a stable complex with the laminin, nectin, sex-hormone binding globulin (LNS) domain of Nrxn1β. Furthermore, the negative-stain electron microscopy reconstruction of hexameric full-length Cbln1 at 13 Å resolution and that of the Cbln4/Nrxn1β complex at 19 Å resolution suggest that Nrxn1β binds to the N-terminal region of Cbln4, probably through strand β10 of the S4 insert.


    Related Citations: 
    • Cbln1 and Cbln4 Are Structurally Similar but Differ in GluD2 Binding Interactions.
      Zhong, C.,Shen, J.,Zhang, H.,Li, G.,Shen, S.,Wang, F.,Hu, K.,Cao, L.,He, Y.,Ding, J.
      (2017) Cell Rep 20: 2328


    Organizational Affiliation

    National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, P.R. China. Electronic address: czhong@sibcb.ac.cn.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cerebellin-4
A
186Mus musculusMutation(s): 0 
Gene Names: Cbln4 (Cblnl1)
Find proteins for Q8BME9 (Mus musculus)
Go to UniProtKB:  Q8BME9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
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: 2.8 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.207 
  • Space Group: P 43 3 2
Unit Cell:
Length (Å)Angle (°)
a = 132.357α = 90.00
b = 132.357β = 90.00
c = 132.357γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data scaling
REFMACrefinement
PHENIXphasing
HKL-3000data processing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
the National Natural Science Foundation of ChinaChina31370726
the Ministry of Science and Technology of ChinaChina2013CB910404

Revision History 

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Database references
  • Version 1.2: 2018-01-17
    Type: Database references