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- EMDB-6666: The hexamer of full-length Cbln4 in complex with the LNS domain o... -

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Basic information

Entry
Database: EMDB / ID: EMD-6666
TitleThe hexamer of full-length Cbln4 in complex with the LNS domain of Nrxn1beta
Map data
SampleNrxn1beta != Cbln4

Nrxn1beta

  • Complex: Cbln4
    • Protein or peptide: Cbln4
  • Complex: Nrxn1beta
    • Protein or peptide: Nrxn1beta
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 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: 0.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6666.png

Downloads & links

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Map

FileDownload / File: emd_6666.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.)
3.48 Å/pix.
x 64 pix.
= 222.72 Å		3.48 Å/pix.
x 64 pix.
= 222.72 Å		3.48 Å/pix.
x 64 pix.
= 222.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.48 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6 / Movie #1: 0.6
Minimum - Maximum-0.6238839 - 3.1701295
Average (Standard dev.)0.040619545 (±0.25700653)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-32-32-32
Dimensions646464
Spacing646464
CellA=B=C: 222.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.483.483.48
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z222.720222.720222.720
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-32-32-32
NC/NR/NS646464
D min/max/mean-0.6243.1700.041

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Supplemental data

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Sample components

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Entire : Nrxn1beta

EntireName: Nrxn1beta
Components
  • Complex: Cbln4
    • Protein or peptide: Cbln4
  • Complex: Nrxn1beta
    • Protein or peptide: Nrxn1beta

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Supramolecule #1: Cbln4

SupramoleculeName: Cbln4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant plasmid: pCDH

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Supramolecule #2: Nrxn1beta

SupramoleculeName: Nrxn1beta / type: complex / ID: 2 / Parent: 0 / Macromolecule list: #2

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Macromolecule #1: Cbln4

MacromoleculeName: Cbln4 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
LQHHHHHHHH ASQNDTEPIV LEGKCLVVCD SNPATDSKGS SSSPLGISVR AANSKVAFSA VRSTNHEPSE MSNKTRIIYF DQILVNVGNF FTLESVFVAP RKGIYSFSFH VIKVYQSQTI QVNLMLNGKP VISAFAGDKD VTREAATNGV LLYLDKEDKV YLKLEKGNLL GGWQYSTFSG FLVFPL

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Macromolecule #2: Nrxn1beta

MacromoleculeName: Nrxn1beta / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: mgshhhhhhh hgsdydiptt enlyfqgssl rgghagttyi fskgggqity kwppndrpst radrlaigfs tvqkeavlvr vdsssglgdy lelhihqgki gvkfnvgtdd iaieesnaii ndgkyhvvrf trsggnatlq vdswpviery pagnndnerl aiarqripyr ...String:
mgshhhhhhh hgsdydiptt enlyfqgssl rgghagttyi fskgggqity kwppndrpst radrlaigfs tvqkeavlvr vdsssglgdy lelhihqgki gvkfnvgtdd iaieesnaii ndgkyhvvrf trsggnatlq vdswpviery pagnndnerl aiarqripyr lgrvvdewll dkgrqltifn sqatiiiggk eqgqpfqgql sglyynglkv lnmaaendan iaivgnvrlv gevpssefws hpqfek

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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 12
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9148
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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