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- EMDB-6665: The hexamer of full-length Cbln1 -

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Basic information

Entry
Database: EMDB / ID: 6665
TitleThe hexamer of full-length Cbln1
Map data
SampleCbln1:
SourceRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / 13 Å resolution
AuthorsZhong C / Li G / Zhang H / Cao L / He Y / Ding J
CitationJournal: Cell Rep / Year: 2017
Title: Cbln1 and Cbln4 Are Structurally Similar but Differ in GluD2 Binding Interactions.
Authors: Chen Zhong / Jinlong Shen / Huibing Zhang / Guangyi Li / Senlin Shen / Fang Wang / Kuan Hu / Longxing Cao / Yongning He / Jianping Ding
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 ...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.
DateDeposition: Nov 5, 2016 / Header (metadata) release: Sep 13, 2017 / Map release: Sep 13, 2017 / Last update: Sep 13, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6665.map.gz (map file in CCP4 format, 1049 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
64 pix
2.96 Å/pix.
= 189.44 Å
64 pix
2.96 Å/pix.
= 189.44 Å
64 pix
2.96 Å/pix.
= 189.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.96 Å
Density
Contour Level:0.5 (by author), 0.5 (movie #1):
Minimum - Maximum-0.5862303 - 2.9113793
Average (Standard dev.)0.038173668 (0.22286722)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions646464
Origin-32-32-32
Limit313131
Spacing646464
CellA=B=C: 189.44 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.962.962.96
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z189.440189.440189.440
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-32-32-32
NC/NR/NS646464
D min/max/mean-0.5862.9110.038

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Supplemental data

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Sample components

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Entire Cbln1

EntireName: Cbln1 / Number of components: 2

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Component #1: protein, Cbln1

ProteinName: Cbln1 / Recombinant expression: No
SourceSpecies: Rattus norvegicus (Norway rat)
Source (engineered)Expression System: Homo sapiens (human) / Vector: pCDH

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Component #2: protein, Cbln1

ProteinName: Cbln1 / Recombinant expression: No
Source (engineered)Expression System: Rattus norvegicus (Norway rat)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI EAGLE (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 41994
3D reconstructionResolution: 13 Å / Resolution method: FSC 0.143 CUT-OFF

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