+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36853 | |||||||||
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Title | Structure of human CNTN2 immunoglobulin domains 1-6 homo-dimer | |||||||||
Map data | ||||||||||
Sample |
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Keywords | neural 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 / synapse organization / myelin sheath / postsynaptic membrane / cell adhesion / axon / synapse / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Zhang ZZ | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: Structure of human CNTN2 immunoglobulin domains 1-6 homo-dimer Authors: Zhang ZZ | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36853.map.gz | 230.3 MB | EMDB map data format | |
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Header (meta data) | emd-36853-v30.xml emd-36853.xml | 13.1 KB 13.1 KB | Display Display | EMDB header |
Images | emd_36853.png | 39.6 KB | ||
Filedesc metadata | emd-36853.cif.gz | 5.6 KB | ||
Others | emd_36853_half_map_1.map.gz emd_36853_half_map_2.map.gz | 226.2 MB 226.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36853 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36853 | HTTPS FTP |
-Validation report
Summary document | emd_36853_validation.pdf.gz | 854 KB | Display | EMDB validaton report |
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Full document | emd_36853_full_validation.pdf.gz | 853.5 KB | Display | |
Data in XML | emd_36853_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | emd_36853_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36853 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36853 | HTTPS FTP |
-Related structure data
Related structure data | 8k3jMC 8k53C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_36853.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.92 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_36853_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_36853_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : CNTN2
Entire | Name: CNTN2 |
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Components |
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-Supramolecule #1: CNTN2
Supramolecule | Name: CNTN2 / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Contactin-2
Macromolecule | Name: Contactin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 107.585203 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 4 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: TUNGSTEN HAIRPIN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 292684 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |