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- EMDB-5270: The entire ectodomain of bovine Nrx1alpha -

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Basic information

Entry
Database: EMDB / ID: EMD-5270
TitleThe entire ectodomain of bovine Nrx1alpha
Map dataThis is a 3-D map of the entire ectodomain of bovine Nrx1alpha
Sample
  • Sample: an ectodomain fragment of alpha-neurexin 1
  • Protein or peptide: Neurexin
Keywordssynapse / neulexin / neuroligin / single particle reconstruction
Function / homologycell adhesion
Function and homology information
Biological speciesunidentified (others)
Methodsingle particle reconstruction / negative staining
AuthorsTanaka H / Nogi T / Yasui N / Iwasaki K / Takagi J
CitationJournal: 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
DepositionMar 24, 2011-
Header (metadata) releaseJun 23, 2011-
Map releaseJun 27, 2011-
UpdateSep 23, 2011-
Current statusSep 23, 2011Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 7.59
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 7.59
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5270_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5270.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a 3-D map of the entire ectodomain of bovine Nrx1alpha
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.2 Å/pix.
x 200 pix.
= 440. Å		2.2 Å/pix.
x 200 pix.
= 440. Å		2.2 Å/pix.
x 200 pix.
= 440. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.59 / Movie #1: 7.59
Minimum - Maximum-11.7317 - 29.890899999999998
Average (Standard dev.)-0.0000000071204 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions200200200
Spacing200200200
CellA=B=C: 440 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.22.22.2
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z440.000440.000440.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS200200200
D min/max/mean-11.73229.891-0.000

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Supplemental data

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Sample components

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Entire : an ectodomain fragment of alpha-neurexin 1

EntireName: 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

SupramoleculeName: 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
Molecular weightExperimental: 140 KDa / Theoretical: 140 KDa / Method: SDS-PAGE

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Macromolecule #1: Neurexin

MacromoleculeName: Neurexin / type: protein_or_peptide / ID: 1 / Name.synonym: Neurexin / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: unidentified (others) / synonym: bovine / Organelle: Synapse / Location in cell: Cell membrane
Molecular weightExperimental: 140 KDa / Theoretical: 140 KDa
Recombinant expressionOrganism: CHO Cells / Recombinant plasmid: pcDNA3.1
SequenceGO: cell adhesion

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

StainingType: NEGATIVE / Details: 2% w/v uranyl acetate
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeHITACHI H-9500SD
TemperatureAverage: 293 K
Electron beamAcceleration voltage: 300 kV / Electron source: LAB6
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: Normal HITACHI side entry holder / Specimen holder model: OTHER

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Image processing

Final reconstructionSoftware - Name: EMAN

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Atomic model buiding 1

Initial modelPDB ID:

3asi

RefinementSpace: REAL

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