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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 / 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
: / 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: To Be Published
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
DepositionApr 3, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release

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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

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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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