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- EMDB-36896: Structure of the Dimeric Human CNTN2 Ig 1-6-FNIII 1-2 Domain in a... -

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Basic information

Entry
Database: EMDB / ID: EMD-36896
TitleStructure of the Dimeric Human CNTN2 Ig 1-6-FNIII 1-2 Domain in an Asymmetric State
Map data
Sample
  • Cell: CNTN2
    • Protein or peptide: Contactin-2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsneural cell adhesion / CELL ADHESION
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 / dendrite self-avoidance / cell-cell adhesion mediator activity / protein localization to juxtaparanode region of axon / NrCAM interactions / 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 / dendrite self-avoidance / cell-cell adhesion mediator activity / protein localization to juxtaparanode region of axon / NrCAM interactions / 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 / axon guidance / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsZhang ZZ
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82201315 China
National Natural Science Foundation of China (NSFC)K19381005 China
CitationJournal: To Be Published
Title: Structure of human CNTN2 immunoglobulin domains 1-6 homo-dimer
Authors: Zhang ZZ / Shi ZB / Wang DP
History
DepositionJul 21, 2023-
Header (metadata) releaseDec 6, 2023-
Map releaseDec 6, 2023-
UpdateDec 6, 2023-
Current statusDec 6, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36896.png

Downloads & links

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Map

FileDownload / File: emd_36896.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.92 Å
Density
Contour LevelBy AUTHOR: 0.125
Minimum - Maximum-2.3791995 - 3.935342
Average (Standard dev.)0.00018387337 (±0.04062894)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 368.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36896_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36896_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CNTN2

EntireName: CNTN2
Components
  • Cell: CNTN2
    • Protein or peptide: Contactin-2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: CNTN2

SupramoleculeName: CNTN2 / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Contactin-2

MacromoleculeName: Contactin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 107.585203 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SQTTFGPVFE DQPLSVLFPE ESTEEQVLLA CRARASPPAT YRWKMNGTEM KLEPGSRHQL VGGNLVIMNP TKAQDAGVYQ CLASNPVGT VVSREAILRF GFLQEFSKEE RDPVKAHEGW GVMLPCNPPA HYPGLSYRWL LNEFPNFIPT DGRHFVSQTT G NLYIARTN ...String:
SQTTFGPVFE DQPLSVLFPE ESTEEQVLLA CRARASPPAT YRWKMNGTEM KLEPGSRHQL VGGNLVIMNP TKAQDAGVYQ CLASNPVGT VVSREAILRF GFLQEFSKEE RDPVKAHEGW GVMLPCNPPA HYPGLSYRWL LNEFPNFIPT DGRHFVSQTT G NLYIARTN ASDLGNYSCL ATSHMDFSTK SVFSKFAQLN LAAEDTRLFA PSIKARFPAE TYALVGQQVT LECFAFGNPV PR IKWRKVD GSLSPQWTTA EPTLQIPSVS FEDEGTYECE AENSKGRDTV QGRIIVQAQP EWLKVISDTE ADIGSNLRWG CAA AGKPRP TVRWLRNGEP LASQNRVEVL AGDLRFSKLS LEDSGMYQCV AENKHGTIYA SAELAVQALA PDFRLNPVRR LIPA ARGGE ILIPCQPRAA PKAVVLWSKG TEILVNSSRV TVTPDGTLII RNISRSDEGK YTCFAENFMG KANSTGILSV RDATK ITLA PSSADINLGD NLTLQCHASH DPTMDLTFTW TLDDFPIDFD KPGGHYRRTN VKETIGDLTI LNAQLRHGGK YTCMAQ TVV DSASKEATVL VRGPPGPPGG VVVRDIGDTT IQLSWSRGFD NHSPIAKYTL QARTPPAGKW KQVRTNPANI EGNAETA QV LGLTPWMDYE FRVIASNILG TGEPSGPSSK IRTREAAPSV APSGLSGGGG APGELIVNWT PMSREYQNGD GFGYLLSF R RQGSTHWQTA RVPGADAQYF VYSNESVRPY TPFEVKIRSY NRRGDGPESL TALVYSAEEE PRVAPTKVWA KGVSSSEMN VTWEPVQQDM NGILLGYEIR YWKAGDKEAA ADRVRTAGLD TSARVSGLHP NTKYHVTVRA YNRAGTGPAS PSANATTMKP PPRRPPGNI SWTFSSSSLS IKWDPVVPFR NESAVTGYKM LYQNDLHLTP TLHLTGKNWI EIPVPEDIGH ALVQIRTTGP G GDGIPAEV HIVRNGGTSM MVEN

UniProtKB: Contactin-2

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 292684

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