Journal: PLoS One / Year: 2011 Title: Structural basis for variant-specific neuroligin-binding by α-neurexin. Authors: Hiroki Tanaka / Terukazu Nogi / Norihisa Yasui / Kenji Iwasaki / Junichi Takagi / Abstract: Neurexins (Nrxs) are presynaptic membrane proteins with a single membrane-spanning domain that mediate asymmetric trans-synaptic cell adhesion by binding to their postsynaptic receptor neuroligins. ...Neurexins (Nrxs) are presynaptic membrane proteins with a single membrane-spanning domain that mediate asymmetric trans-synaptic cell adhesion by binding to their postsynaptic receptor neuroligins. α-Nrx has a large extracellular region comprised of multiple copies of laminin, neurexin, sex-hormone-binding globulin (LNS) domains and epidermal growth factor (EGF) modules, while that of β-Nrx has but a single LNS domain. It has long been known that the larger α-Nrx and the shorter β-Nrx show distinct binding behaviors toward different isoforms/variants of neuroligins, although the underlying mechanism has yet to be elucidated. Here, we describe the crystal structure of a fragment corresponding to the C-terminal one-third of the Nrx1α ectodomain, consisting of LNS5-EGF3-LNS6. The 2.3 Å-resolution structure revealed the presence of a domain configuration that was rigidified by inter-domain contacts, as opposed to the more common flexible "beads-on-a-string" arrangement. Although the neuroligin-binding site on the LNS6 domain was completely exposed, the location of the α-Nrx specific LNS5-EGF3 segment proved incompatible with the loop segment inserted in the B+ neuroligin variant, which explains the variant-specific neuroligin recognition capability observed in α-Nrx. This, combined with a low-resolution molecular envelope obtained by a single particle reconstruction performed on negatively stained full-length Nrx1α sample, allowed us to derive a structural model of the α-Nrx ectodomain. This model will help us understand not only how the large α-Nrx ectodomain is accommodated in the synaptic cleft, but also how the trans-synaptic adhesion mediated by α- and β-Nrxs could differentially affect synaptic structure and function.
History
Deposition
Mar 24, 2011
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Header (metadata) release
Jun 23, 2011
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Map release
Jun 27, 2011
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Update
Sep 23, 2011
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Current status
Sep 23, 2011
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Download / File: emd_5270.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
This is a 3-D map of the entire ectodomain of bovine Nrx1alpha
Voxel size
X=Y=Z: 2.2 Å
Density
Contour Level
By AUTHOR: 7.59 / Movie #1: 7.59
Minimum - Maximum
-11.7317 - 29.890899999999998
Average (Standard dev.)
-0.0000000071204 (±1.0)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
-100
-100
-100
Dimensions
200
200
200
Spacing
200
200
200
Cell
A=B=C: 440 Å α=β=γ: 90 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
2.2
2.2
2.2
M x/y/z
200
200
200
origin x/y/z
0.000
0.000
0.000
length x/y/z
440.000
440.000
440.000
α/β/γ
90.000
90.000
90.000
start NX/NY/NZ
-62
-62
-62
NX/NY/NZ
125
125
125
MAP C/R/S
1
2
3
start NC/NR/NS
-100
-100
-100
NC/NR/NS
200
200
200
D min/max/mean
-11.732
29.891
-0.000
-
Supplemental data
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Sample components
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Entire : an ectodomain fragment of alpha-neurexin 1
Entire
Name: an ectodomain fragment of alpha-neurexin 1
Components
Sample: an ectodomain fragment of alpha-neurexin 1
Protein or peptide: Neurexin
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Supramolecule #1000: an ectodomain fragment of alpha-neurexin 1
Supramolecule
Name: an ectodomain fragment of alpha-neurexin 1 / type: sample / ID: 1000 Details: The sample was subjected to a size exclusion chromatography before negatively staining Oligomeric state: monomer / Number unique components: 1
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