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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9563 | |||||||||
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Title | IPET 3D reconstruction of a single CNTNAP2: conformation #1 | |||||||||
![]() | IPET 3D reconstruction of a single CNTNAP2: conformation #1 | |||||||||
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Function / homology | ![]() 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 | |||||||||
Biological species | ![]() | |||||||||
Method | electron tomography / negative staining / Resolution: 16.3 Å | |||||||||
![]() | Lu 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 | ![]()
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![]() | ![]() 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 |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.6 KB 20.6 KB | Display Display | ![]() |
Images | ![]() | 38.6 KB | ||
Others | ![]() ![]() | 59.6 MB 20.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6717C ![]() 9543C ![]() 9544C ![]() 9545C ![]() 9546C ![]() 9547C ![]() 9548C ![]() 9549C ![]() 9550C ![]() 9551C ![]() 9552C ![]() 9553C ![]() 9554C ![]() 9555C ![]() 9556C ![]() 9557C ![]() 9558C ![]() 9559C ![]() 9560C ![]() 9561C ![]() 9562C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | IPET 3D reconstruction of a single CNTNAP2: conformation #1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.94 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: IPET 3D reconstruction of a single CNTNAP2: conformation...
File | emd_9563_additional_1.map | ||||||||||||
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Annotation | IPET 3D reconstruction of a single CNTNAP2: conformation #1, additional map #1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: IPET 3D reconstruction of a single CNTNAP2: conformation...
File | emd_9563_additional_2.map | ||||||||||||
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Annotation | IPET 3D reconstruction of a single CNTNAP2: conformation #1, additional map #2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : CNTNAP2
Entire | Name: CNTNAP2 |
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Components |
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-Supramolecule #1: CNTNAP2
Supramolecule | Name: 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). |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
Molecular weight | Theoretical: 134 kDa/nm |
-Experimental details
-Structure determination
Method | negative staining |
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![]() | electron tomography |
Aggregation state | particle |
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Sample preparation
Concentration | 0.005 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Staining | Type: NEGATIVE / Material: uranium formate / Details: 1% (w/v) uranyl formate | ||||||||||||
Grid | Model: 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 | ||||||||||||
Details | This sample was monodisperse. | ||||||||||||
Sectioning | Other: NO SECTIONING |
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Electron microscopy
Microscope | ZEISS LIBRA120PLUS |
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Specialist optics | Energy filter - Name: Zeiss in-column Omega filter / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV |
Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 89 / Average electron dose: 3.0 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination 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 stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER |
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Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 16.3 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IPET / Number images used: 89 |
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CTF correction | Software - Name: TOMOCTF |