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Open data
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Basic information
Entry | Database: PDB / ID: 9ba5 | ||||||
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Title | Cross-linked Contactin 2 Ig1-Ig6 | ||||||
![]() | Contactin-2 | ||||||
![]() | MEMBRANE PROTEIN / contactins / adhesion molecule / protein structure / conformational changes / homodimer | ||||||
Function / homology | ![]() 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 / protein localization to juxtaparanode region of axon / dendrite self-avoidance / NrCAM interactions / cell-cell adhesion mediator activity / 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 / protein localization to juxtaparanode region of axon / dendrite self-avoidance / NrCAM interactions / cell-cell adhesion mediator activity / 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 / synapse organization / axon guidance / brain development / myelin sheath / postsynaptic membrane / cell adhesion / axon / synapse / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.51 Å | ||||||
![]() | Liu, J.L. / Fan, S.F. / Ren, G.R. / Rudenko, G.R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular mechanism of Contactin 2 homophilic interaction Authors: Fan, S.F. / Liu, J.L. / Chofflett, N.C. / Bailey, A.B. / Russell, W.R. / Zhang, Z.Z. / Takahashi, H.T. / Ren, G.R. / Rudenko, G.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 215.5 KB | Display | ![]() |
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PDB format | ![]() | 167 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 47.3 KB | Display | |
Data in CIF | ![]() | 70.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 44396MC ![]() 9ba4C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 65394.629 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Sugar | ChemComp-NAG / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Contactin 2 Ig1-Ig6 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT | |||||||||||||||
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Source (natural) | Organism: ![]() | |||||||||||||||
Source (recombinant) | Organism: ![]() | |||||||||||||||
Buffer solution | pH: 8 / Details: 20 mM HEPES pH 8.0, 50 mM NaCl | |||||||||||||||
Buffer component |
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Specimen | Conc.: 0.025 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 281 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 7.39 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4297 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98082 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT | ||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 100.14 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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