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Yorodumi- PDB-5zo2: Crystal structure of mouse nectin-like molecule 4 (mNecl-4) full ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zo2 | |||||||||
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Title | Crystal structure of mouse nectin-like molecule 4 (mNecl-4) full ectodomain in complex with mouse nectin-like molecule 1 (mNecl-1) Ig1 domain, 3.3A | |||||||||
Components |
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Keywords | CELL ADHESION / cell adhesion molecule / glycoprotein / Ig domain / SynCam / CADM / Nectin-like / Necl-4 / Necl-1 / axon / Schwann Cell / Molecular Replacement / myelogenesis / heterogeneous dimer | |||||||||
Function / homology | Function and homology information Nectin/Necl trans heterodimerization / : / vascular endothelial growth factor receptor 1 binding / negative regulation of peptidyl-tyrosine phosphorylation / negative regulation of vascular endothelial growth factor signaling pathway / Adherens junctions interactions / regulation of Rac protein signal transduction / cell-cell contact zone / vascular endothelial growth factor receptor 2 binding / regulation of wound healing ...Nectin/Necl trans heterodimerization / : / vascular endothelial growth factor receptor 1 binding / negative regulation of peptidyl-tyrosine phosphorylation / negative regulation of vascular endothelial growth factor signaling pathway / Adherens junctions interactions / regulation of Rac protein signal transduction / cell-cell contact zone / vascular endothelial growth factor receptor 2 binding / regulation of wound healing / regulation of cell motility / parallel fiber to Purkinje cell synapse / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / negative regulation of vascular endothelial growth factor receptor signaling pathway / negative regulation of peptidyl-threonine phosphorylation / homophilic cell adhesion via plasma membrane adhesion molecules / cell leading edge / negative regulation of protein phosphorylation / regulation of protein phosphorylation / receptor tyrosine kinase binding / cell-cell junction / protein localization / regulation of cell population proliferation / protein phosphatase binding / protein homodimerization activity / membrane Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.29 Å | |||||||||
Authors | Liu, X. / An, T. / Li, D. / Fan, Z. / Xiang, P. / Li, C. / Ju, W. / Li, J. / Hu, G. / Qin, B. ...Liu, X. / An, T. / Li, D. / Fan, Z. / Xiang, P. / Li, C. / Ju, W. / Li, J. / Hu, G. / Qin, B. / Yin, B. / Wojdyla, J.A. / Wang, M. / Yuan, J. / Qiang, B. / Shu, P. / Cui, S. / Peng, X. | |||||||||
Funding support | China, 2items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019 Title: Structure of the heterophilic interaction between the nectin-like 4 and nectin-like 1 molecules. Authors: Liu, X. / An, T. / Li, D. / Fan, Z. / Xiang, P. / Li, C. / Ju, W. / Li, J. / Hu, G. / Qin, B. / Yin, B. / Wojdyla, J.A. / Wang, M. / Yuan, J. / Qiang, B. / Shu, P. / Cui, S. / Peng, X. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zo2.cif.gz | 132.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zo2.ent.gz | 100.8 KB | Display | PDB format |
PDBx/mmJSON format | 5zo2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zo2_validation.pdf.gz | 767.8 KB | Display | wwPDB validaton report |
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Full document | 5zo2_full_validation.pdf.gz | 781.8 KB | Display | |
Data in XML | 5zo2_validation.xml.gz | 24.4 KB | Display | |
Data in CIF | 5zo2_validation.cif.gz | 32.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zo/5zo2 ftp://data.pdbj.org/pub/pdb/validation_reports/zo/5zo2 | HTTPS FTP |
-Related structure data
Related structure data | 5zo1C 1z9mS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 33303.145 Da / Num. of mol.: 2 / Fragment: extracellular domains (Ig1-Ig3) / Mutation: N31Q, N262Q, N286Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Tissue: Brain Kidney Spleen / Gene: Cadm4, Igsf4c, Necl4, Tsll2 / Organ: Brain Kidney Spleen / Plasmid: pFast-Bac 1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8R464 #2: Protein | | Mass: 15998.754 Da / Num. of mol.: 1 / Fragment: Ig domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Tissue: Brain / Gene: Cadm3, Igsf4b, Necl1, Syncam3, Tsll1 / Organ: Brain / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / References: UniProt: Q99N28 #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.98 Å3/Da / Density % sol: 75.78 % / Description: hexagonal prisms-like crystals |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2M calcium acetate, 0.1M HEPES Sodium Salt ,pH7.5, 10% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97776 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97776 Å / Relative weight: 1 |
Reflection | Resolution: 3.29→49.836 Å / Num. obs: 19407 / % possible obs: 97.19 % / Observed criterion σ(I): -3 / Redundancy: 5.68 % / Biso Wilson estimate: 64.79 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.224 / Χ2: 0.98 / Net I/σ(I): 6.96 |
Reflection shell | Resolution: 3.29→3.49 Å / Redundancy: 5.74 % / Rmerge(I) obs: 1.074 / Mean I/σ(I) obs: 1.64 / Num. unique obs: 3096 / CC1/2: 0.613 / Χ2: 0.89 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Z9M Resolution: 3.29→49.84 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.49
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Displacement parameters | Biso mean: 65.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.29→49.84 Å
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Refine LS restraints |
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LS refinement shell |
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