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

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Basic information

Entry
Database: EMDB / ID: EMD-6665
TitleThe hexamer of full-length Cbln1
Map data
Sample
  • Complex: Cbln1
    • Protein or peptide: Cbln1
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / negative staining / Resolution: 13.0 Å
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.
History
DepositionNov 5, 2016-
Header (metadata) releaseSep 13, 2017-
Map releaseSep 13, 2017-
UpdateSep 13, 2017-
Current statusSep 13, 2017Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • 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

emd_6665.png

Downloads & links

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Map

FileDownload / File: emd_6665.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5 / Movie #1: 0.5
Minimum - Maximum-0.5862303 - 2.9113793
Average (Standard dev.)0.038173668 (±0.22286722)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-32-32-32
Dimensions646464
Spacing646464
CellA=B=C: 189.44 Å
α=β=γ: 90.0 °

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
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
Components
  • Complex: Cbln1
    • Protein or peptide: Cbln1

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Supramolecule #1: Cbln1

SupramoleculeName: Cbln1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant plasmid: pCDH

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Macromolecule #1: Cbln1

MacromoleculeName: Cbln1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GTHHHHHHHH GSQNETEPIV LEGKCLVVCD SNPTSDPTGT ALGISVRSGS AKVAFSAIRS TNHEPSEMSN RTMIIYFDQV LVNIGNNFDS ERSTFIAPRK GIYSFNFHVV KVYNRQTIQV SLMLNGWPVI SAFAGDQDVT REAASNGVLI QMEKGDRAYL KLERGNLMGG WKYSTFSGFL VFPL

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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

BufferpH: 8
StainingType: NEGATIVE / Material: 0.75% uranyl formate
VitrificationCryogen name: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 13.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 41994
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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