[English] 日本語
Yorodumi
- EMDB-9560: IPET 3D reconstruction of a single CNTNAP2: conformation #4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-9560
TitleIPET 3D reconstruction of a single CNTNAP2: conformation #4
Map dataIPET 3D reconstruction of a single CNTNAP2: conformation #4
Sample
  • Complex: CNTNAP2
Function / homology
Function and homology information


limbic system development / clustering of voltage-gated potassium channels / neuron recognition / vocal learning / protein localization to juxtaparanode region of axon / paranodal junction / superior temporal gyrus development / thalamus development / vocalization behavior / paranode region of axon ...limbic system development / clustering of voltage-gated potassium channels / neuron recognition / vocal learning / protein localization to juxtaparanode region of axon / paranodal junction / superior temporal gyrus development / thalamus development / vocalization behavior / paranode region of axon / striatum development / juxtaparanode region of axon / adult behavior / transmission of nerve impulse / social behavior / positive regulation of gap junction assembly / axolemma / prepulse inhibition / voltage-gated potassium channel complex / neuron projection morphogenesis / learning / synaptic membrane / brain development / cerebral cortex development / neuron projection development / protease binding / perikaryon / transmembrane transporter binding / cell population proliferation / early endosome / cell adhesion / axon / neuronal cell body / dendrite / Golgi apparatus / enzyme binding / cell surface / membrane
Similarity search - Function
Neurexin/syndecan/glycophorin C / : / putative band 4.1 homologues' binding motif / Laminin G domain / Laminin G domain profile. / Laminin G domain / Laminin G domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. ...Neurexin/syndecan/glycophorin C / : / putative band 4.1 homologues' binding motif / Laminin G domain / Laminin G domain profile. / Laminin G domain / Laminin G domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Contactin-associated protein-like 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodelectron tomography / negative staining / Resolution: 16.5 Å
AuthorsLu Z / Reddy MS / Liu JF / Kalichava A / Liu JK / Zhang L / Chen F / Wang Y / Holthauzen LM / Seshadrinathan S ...Lu Z / Reddy MS / Liu JF / Kalichava A / Liu JK / Zhang L / Chen F / Wang Y / Holthauzen LM / Seshadrinathan S / Zhong XY / Ren G / Rudenko G
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental HealthR01MH077303 United States
Department of Energy (United States)DE-AC02-05CH11231 United States
CitationJournal: J Biol Chem / Year: 2016
Title: Molecular Architecture of Contactin-associated Protein-like 2 (CNTNAP2) and Its Interaction with Contactin 2 (CNTN2).
Authors: Zhuoyang Lu / M V V V Sekhar Reddy / Jianfang Liu / Ana Kalichava / Jiankang Liu / Lei Zhang / Fang Chen / Yun Wang / Luis Marcelo F Holthauzen / Mark A White / Suchithra Seshadrinathan / ...Authors: Zhuoyang Lu / M V V V Sekhar Reddy / Jianfang Liu / Ana Kalichava / Jiankang Liu / Lei Zhang / Fang Chen / Yun Wang / Luis Marcelo F Holthauzen / Mark A White / Suchithra Seshadrinathan / Xiaoying Zhong / Gang Ren / Gabby Rudenko /
Abstract: Contactin-associated protein-like 2 (CNTNAP2) is a large multidomain neuronal adhesion molecule implicated in a number of neurological disorders, including epilepsy, schizophrenia, autism spectrum ...Contactin-associated protein-like 2 (CNTNAP2) is a large multidomain neuronal adhesion molecule implicated in a number of neurological disorders, including epilepsy, schizophrenia, autism spectrum disorder, intellectual disability, and language delay. We reveal here by electron microscopy that the architecture of CNTNAP2 is composed of a large, medium, and small lobe that flex with respect to each other. Using epitope labeling and fragments, we assign the F58C, L1, and L2 domains to the large lobe, the FBG and L3 domains to the middle lobe, and the L4 domain to the small lobe of the CNTNAP2 molecular envelope. Our data reveal that CNTNAP2 has a very different architecture compared with neurexin 1α, a fellow member of the neurexin superfamily and a prototype, suggesting that CNTNAP2 uses a different strategy to integrate into the synaptic protein network. We show that the ectodomains of CNTNAP2 and contactin 2 (CNTN2) bind directly and specifically, with low nanomolar affinity. We show further that mutations in CNTNAP2 implicated in autism spectrum disorder are not segregated but are distributed over the whole ectodomain. The molecular shape and dimensions of CNTNAP2 place constraints on how CNTNAP2 integrates in the cleft of axo-glial and neuronal contact sites and how it functions as an organizing and adhesive molecule.
History
DepositionOct 3, 2016-
Header (metadata) releaseOct 19, 2016-
Map releaseOct 19, 2016-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9560.png

Downloads & links

-
Map

FileDownload / File: emd_9560.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIPET 3D reconstruction of a single CNTNAP2: conformation #4
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 256 pix.
= 240.64 Å		0.94 Å/pix.
x 256 pix.
= 240.64 Å		0.94 Å/pix.
x 256 pix.
= 240.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelMovie #1: 1
Minimum - Maximum-2.5783048 - 2.6590903
Average (Standard dev.)-0.016053105 (±0.28186613)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 240.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.940.940.94
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z240.640240.640240.640
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-2.5782.659-0.016

-
Supplemental data

-
Additional map: IPET 3D reconstruction of a single CNTNAP2: conformation...

Fileemd_9560_additional_1.map
AnnotationIPET 3D reconstruction of a single CNTNAP2: conformation #4, additional map #1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: IPET 3D reconstruction of a single CNTNAP2: conformation...

Fileemd_9560_additional_2.map
AnnotationIPET 3D reconstruction of a single CNTNAP2: conformation #4, additional map #2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : CNTNAP2

EntireName: CNTNAP2
Components
  • Complex: CNTNAP2

-
Supramolecule #1: CNTNAP2

SupramoleculeName: CNTNAP2 / type: complex / ID: 1 / Parent: 0
Details: Human contactin-associated protein-like 2 (CNTNAP2) ectodomain (or fragments) with a C-terminal ASTSHHHHHH tag were produced using baculovirus-mediated overexpression in High Five cells in ...Details: Human contactin-associated protein-like 2 (CNTNAP2) ectodomain (or fragments) with a C-terminal ASTSHHHHHH tag were produced using baculovirus-mediated overexpression in High Five cells in Insect-XPRESS+L-Glutamine medium (Lonza).
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper) / Recombinant cell: High Five / Recombinant plasmid: baculovirus
Molecular weightTheoretical: 134 kDa/nm

-
Experimental details

-
Structure determination

Methodnegative staining
Processingelectron tomography
Aggregation stateparticle

-
Sample preparation

Concentration0.005 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
25.0 mMC4H11NO3Tris
100.0 mMNaClsodium chloride
3.0 mMCaCl2calcium chloride
StainingType: NEGATIVE / Material: uranium formate / Details: 1% (w/v) uranyl formate
GridModel: EMSCF, 200-Cu / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 5.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
DetailsThis sample was monodisperse.
SectioningOther: NO SECTIONING

-
Electron microscopy

MicroscopeZEISS LIBRA120PLUS
Specialist opticsEnergy filter - Name: Zeiss in-column Omega filter / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 0.6 µm / Nominal defocus min: 0.1 µm / Nominal magnification: 125000
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER

-
Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 16.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IPET / Number images used: 89
CTF correctionSoftware - Name: TOMOCTF

+
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