[English] 日本語
Yorodumi
- EMDB-44397: Full-length cross-linked Contactin 2 (FN1 apart) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-44397
TitleFull-length cross-linked Contactin 2 (FN1 apart)
Map data
Sample
  • Organelle or cellular component: Contactin-2 full length (Ig1-FN4)
    • Protein or peptide: Contactin 2 (full-length)
Keywordscontactins / adhesion molecule / protein structure / conformational changes / homodimer / MEMBRANE PROTEIN
Function / homology
Function and homology information


establishment of protein localization to juxtaparanode region of axon / presynaptic membrane organization / reduction of food intake in response to dietary excess / L1CAM interactions / clustering of voltage-gated potassium channels / dendrite self-avoidance / protein localization to juxtaparanode region of axon / cell-cell adhesion mediator activity / NrCAM interactions / axon initial segment ...establishment of protein localization to juxtaparanode region of axon / presynaptic membrane organization / reduction of food intake in response to dietary excess / L1CAM interactions / clustering of voltage-gated potassium channels / dendrite self-avoidance / protein localization to juxtaparanode region of axon / cell-cell adhesion mediator activity / NrCAM interactions / axon initial segment / node of Ranvier / juxtaparanode region of axon / NCAM1 interactions / fat cell differentiation / homophilic cell adhesion via plasma membrane adhesion molecules / side of membrane / axon guidance / synapse organization / myelin sheath / postsynaptic membrane / cell adhesion / axon / synapse / plasma membrane
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III ...: / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.77 Å
AuthorsLiu JL / Fan SF / Ren GR / Rudenko GR
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH) United States
CitationJournal: Structure / Year: 2024
Title: Molecular mechanism of contactin 2 homophilic interaction.
Authors: Shanghua Fan / Jianfang Liu / Nicolas Chofflet / Aaron O Bailey / William K Russell / Ziqi Zhang / Hideto Takahashi / Gang Ren / Gabby Rudenko /
Abstract: Contactin 2 (CNTN2) is a cell adhesion molecule involved in axon guidance, neuronal migration, and fasciculation. The ectodomains of CNTN1-CNTN6 are composed of six Ig domains (Ig1-Ig6) and four FN ...Contactin 2 (CNTN2) is a cell adhesion molecule involved in axon guidance, neuronal migration, and fasciculation. The ectodomains of CNTN1-CNTN6 are composed of six Ig domains (Ig1-Ig6) and four FN domains. Here, we show that CNTN2 forms transient homophilic interactions (K ∼200 nM). Cryo-EM structures of full-length CNTN2 and CNTN2_Ig1-Ig6 reveal a T-shaped homodimer formed by intertwined, parallel monomers. Unexpectedly, the horseshoe-shaped Ig1-Ig4 headpieces extend their Ig2-Ig3 tips outwards on either side of the homodimer, while Ig4, Ig5, Ig6, and the FN domains form a central stalk. Cross-linking mass spectrometry and cell-based binding assays confirm the 3D assembly of the CNTN2 homodimer. The interface mediating homodimer formation differs between CNTNs, as do the homophilic versus heterophilic interaction mechanisms. The CNTN family thus encodes a versatile molecular platform that supports a very diverse portfolio of protein interactions and that can be leveraged to strategically guide neural circuit development.
History
DepositionApr 3, 2024-
Header (metadata) releaseJul 17, 2024-
Map releaseJul 17, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_44397.png

Downloads & links

-
Map

FileDownload / File: emd_44397.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 320 pix.
= 336. Å		1.05 Å/pix.
x 320 pix.
= 336. Å		1.05 Å/pix.
x 320 pix.
= 336. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009
Minimum - Maximum-0.018600551 - 2.091152
Average (Standard dev.)0.00053162023 (±0.013535566)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_44397_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_44397_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Contactin-2 full length (Ig1-FN4)

EntireName: Contactin-2 full length (Ig1-FN4)
Components
  • Organelle or cellular component: Contactin-2 full length (Ig1-FN4)
    • Protein or peptide: Contactin 2 (full-length)

-
Supramolecule #1: Contactin-2 full length (Ig1-FN4)

SupramoleculeName: Contactin-2 full length (Ig1-FN4) / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Contactin 2 (full-length)

MacromoleculeName: Contactin 2 (full-length) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: ELGTGLE SQ TTFGPVFE D QPLSVLFPE ESTEEQVLLA CRARASPPA T YRWKMNGT EM KLEPGSR HQL VGGNLV IMNP TKAQD AGVYQ CLAS NPVGTV VSR EAILRFG FL QEFSKEER D PVKAHEGWG VMLPCNPPAH YPGLSYRWL L NEFPNFIP TD ...String:
ELGTGLE SQ TTFGPVFE D QPLSVLFPE ESTEEQVLLA CRARASPPA T YRWKMNGT EM KLEPGSR HQL VGGNLV IMNP TKAQD AGVYQ CLAS NPVGTV VSR EAILRFG FL QEFSKEER D PVKAHEGWG VMLPCNPPAH YPGLSYRWL L NEFPNFIP TD GRHFVSQ TTG NLYIAR TNAS DLGNY SCLAT SHMD FSTKSV FSK FAQLNLA AE DTRLFAPS I KARFPAETY ALVGQQVTLE CFAFGNPVP R IKWRKVDG SL SPQWTTA EPT LQIPSV SFED EGTYE CEAEN SKGR DTVQGR IIV QAQPEWL KV ISDTEADI G SNLRWGCAA AGKPRPTVRW LRNGEPLAS Q NRVEVLAG DL RFSKLSL EDS GMYQCV AENK HGTIY ASAEL AVQA LAPDFR LNP VRRLIPA AR GGEILIPC Q PRAAPKAVV LWSKGTEILV NSSRVTVTP D GTLIIRNI SR SDEGKYT CFA ENFMGK ANST GILSV RDATK ITLA PSSADI NLG DNLTLQC HA SHDPTMDL T FTWTLDDFP IDFDKPGGHY RRTNVKETI G DLTILNAQ LR HGGKYTC MAQ TVVDSA SKEA TVLVR GPPGP PGGV VVRDIG DTT IQLSWSR GF DNHSPIAK Y TLQARTPPA GKWKQVRTNP ANIEGNAET A QVLGLTPW MD YEFRVIA SNI LGTGEP SGPS SKIRT REAAP SVAP SGLSGG GGA PGELIVN WT PMSREYQN G DGFGYLLSF RRQGSTHWQT ARVPGADAQ Y FVYSNESV RP YTPFEVK IRS YNRRGD GPES LTALV YSAEE EPRV APTKVW AKG VSSSEMN VT WEPVQQDM N GILLGYEIR YWKAGDKEAA ADRVRTAGL D TSARVSGL HP NTKYHVT VRA YNRAGT GPAS PSANA TTMKP PPRR PPGNIS WTF SSSSLSI KW DPVVPFRN E SAVTGYKML YQNDLHLTPT LHLTGKNWI E IPVPEDIG HA LVQIRTT GPG GDGIPA EVHI VRN G SASTSHHHHH H

UniProtKB: Contactin-2

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.05 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
10.0 mMHEPES
50.0 mMSodium chlorideNaCl

Details: 10 mM HEPES pH 8.0, 50 mM NaCl
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 281 K / Instrument: LEICA EM GP

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 9049 / Average exposure time: 7.39 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Details: The initial volume was generated by ab initio reconstruction.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.77 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3.0) / Number images used: 78918
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 4.3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more