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- PDB-9ba4: Full-length cross-linked Contactin 2 (CNTN2) -

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Basic information

Entry
Database: PDB / ID: 9ba4
TitleFull-length cross-linked Contactin 2 (CNTN2)
ComponentsContactin-2
KeywordsMEMBRANE PROTEIN / contactins / adhesion molecule / protein structure / conformational changes / homodimer
Function / homology
Function and homology information


establishment of protein localization to juxtaparanode region of axon / presynaptic membrane organization / positive regulation of adenosine receptor signaling pathway / reduction of food intake in response to dietary excess / L1CAM interactions / regulation of astrocyte differentiation / regulation of axon diameter / clustering of voltage-gated potassium channels / cerebral cortex GABAergic interneuron migration / dendrite self-avoidance ...establishment of protein localization to juxtaparanode region of axon / presynaptic membrane organization / positive regulation of adenosine receptor signaling pathway / reduction of food intake in response to dietary excess / L1CAM interactions / regulation of astrocyte differentiation / regulation of axon diameter / clustering of voltage-gated potassium channels / cerebral cortex GABAergic interneuron migration / dendrite self-avoidance / protein localization to juxtaparanode region of axon / NrCAM interactions / cell-cell adhesion mediator activity / central nervous system myelination / positive regulation of protein processing / G protein-coupled adenosine receptor signaling pathway / axon initial segment / NCAM1 interactions / juxtaparanode region of axon / node of Ranvier / regulation of cell morphogenesis / axonal fasciculation / adult walking behavior / fat cell differentiation / homophilic cell adhesion via plasma membrane adhesion molecules / regulation of neuronal synaptic plasticity / negative regulation of neuron differentiation / side of membrane / axon guidance / learning / establishment of localization in cell / synapse organization / protein processing / receptor internalization / microtubule cytoskeleton organization / myelin sheath / carbohydrate binding / postsynaptic membrane / cell adhesion / axon / neuronal cell body / synapse / cell surface / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.54 Å
AuthorsLiu, J.L. / Fan, S.F. / Ren, G.R. / Rudenko, G.R.
Funding support United States, 1items
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, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _em_admin.last_update
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: citation / em_admin ...citation / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.3Nov 20, 2024Group: Data collection / Category: em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Contactin-2
B: Contactin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,82612
Polymers217,3952
Non-polymers3,43110
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Contactin-2 / Axonal glycoprotein TAG-1 / Axonin-1 / Transient axonal glycoprotein 1 / TAX-1


Mass: 108697.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNTN2, AXT, TAG1, TAX1 / Cell (production host): HighFive5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q02246
#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 6 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Contactin-2 full length (Ig1-FN4) / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 8 / Details: 10 mM HEPES pH 8.0, 50 mM NaCl
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMHEPES1
250 mMSodium chlorideNaCl1
SpecimenConc.: 0.05 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: 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
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage 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: 9049
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4cryoSPARC4.3.0CTF correction
7UCSF ChimeraXmodel fitting
8ISOLDEmodel fitting
10cryoSPARC4.3.0initial Euler assignment
11cryoSPARC4.3.0final Euler assignment
13cryoSPARC4.3.03D reconstruction
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86023 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 190.7 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.009715592
ELECTRON MICROSCOPYf_angle_d1.198521254
ELECTRON MICROSCOPYf_chiral_restr0.06982370
ELECTRON MICROSCOPYf_plane_restr0.01092782
ELECTRON MICROSCOPYf_dihedral_angle_d7.29422216

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