PDBsum entry: 3bop

Cell adhesion

PDB-id: 3bop

Main view

Contents

Description

Header details

Header records

References

PROCHECK

Protein chains

168 a.a. *

Waters ×138

* Residue conservation analysis

Tools

Clefts Calculation

Right view	Bottom view

PDB id:

3bop

Name:

Cell adhesion

Title:

Structure of mouse beta-neurexin 2d4

Structure:

Beta-neurexin 2d4. Chain: a, b, c. Fragment: lns domain. Engineered: yes

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Gene: nrxn2. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

UniProt:

Chains A, B, C: Q3TQ54 (Q3TQ54_MOUSE)

Seq:

Struc:

Seq:

353 a.a.

Struc:

168 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 1 residue position (black cross)

Resolution:

3.00Å

R-factor:

0.215

R-free:

0.289

Authors:

J.Koehnke,X.Jin,L.Shapiro

Key ref:

J.Koehnke et al. (2008). Crystal structures of beta-neurexin 1 and beta-neurexin 2 ectodomains and dynamics of splice insertion sequence 4.. Structure, 16, 410-421. [PubMed id: 18334216] [DOI: 10.1016/j.str.2007.12.024]

Date:

17-Dec-07

Release date:

25-Mar-08

Related entries:

3bod
structure of neurexin 1d4

Quick_links

Procheck

Surface

Key reference

DOI no: 10.1016/j.str.2007.12.024

Structure 16:410-421 (2008)

PubMed id: 18334216

Crystal structures of beta-neurexin 1 and beta-neurexin 2 ectodomains and dynamics of splice insertion sequence 4.

J.Koehnke, X.Jin, N.Trbovic, P.S.Katsamba, J.Brasch, G.Ahlsen, P.Scheiffele, B.Honig, A.G.Palmer, L.Shapiro.

ABSTRACT

Presynaptic neurexins (NRXs) bind to postsynaptic neuroligins (NLs) to form Ca(2+)-dependent complexes that bridge neural synapses. beta-NRXs bind NLs through their LNS domains, which contain a single site of alternative splicing (splice site 4) giving rise to two isoforms: +4 and Delta. We present crystal structures of the Delta isoforms of the LNS domains from beta-NRX1 and beta-NRX2, crystallized in the presence of Ca(2+) ions. The Ca(2+)-binding site is disordered in the beta-NRX2 structure, but the 1.7 A beta-NRX1 structure reveals a single Ca(2+) ion, approximately 12 A from the splice insertion site, with one coordinating ligand donated by a glutamic acid from an adjacent beta-NRX1 molecule. NMR studies of beta-NRX1+4 show that the insertion sequence is unstructured, and remains at least partially disordered in complex with NL. These results raise the possibility that beta-NRX insertion sequence 4 may function in roles independent of neuroligin binding.

Selected figure(s)

Figure 5.
Figure 5. Structure of Δ-Isoform LNS Domains from β-NRX1 and β-NRX2
Rainbow ribbon diagrams from blue to red representing the N to C terminus. β Strands are numbered, and the bound Ca^2+ ion in the NRX1 structure is shown as a green sphere. The α-carbon of residue 200, the position of splice insertion 4, is shown as a magenta sphere. An eight-residue stretch in the β9-β10 loop of NRX2 is disordered and is indicated by a dashed yellow line.

Figure 6.
Figure 6. Structure of the Ca^2+ Binding Region from β-NRX1, and Comparison with LNS2 from α-NRX1
(A) Image of 1.7 Å 2F[o]-F[c] electron density contoured at 1.0 σ in the region of the Ca^2+ binding site.
(B) The Ca^2+ ion is ligated by four ligands in the Ca^2+ binding site, one water molecule, and a glutamic acid side chain from a symmetry mate.
(C) Superposition of LNS2 from α-NRX1 (blue) on the β-NRX1 structure (green and yellow) shows that the Ca^2+ binding sites are positioned identically in each LNS domain. Ligation by the N208 side chain appears to be common to all the β-NRX but absent from many other LNS domains of α-NRX.

The above figures are reprinted from an Open Access publication published by Cell Press: Structure (2008, 16, 410-421) copyright 2008.

Figures were selected by an automated process.