+Open data
-Basic information
Entry | Database: PDB / ID: 1ejp | ||||||
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Title | SOLUTION STRUCTURE OF THE SYNDECAN-4 WHOLE CYTOPLASMIC DOMAIN | ||||||
Components | SYNDECAN-4 | ||||||
Keywords | SIGNALING PROTEIN / symmetric-parallel-interwinded dimer | ||||||
Function / homology | Function and homology information Defective B3GALT6 causes EDSP2 and SEMDJL1 / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / Defective EXT2 causes exostoses 2 / Defective EXT1 causes exostoses 1, TRPS2 and CHDS / regulation of fibroblast migration / A tetrasaccharide linker sequence is required for GAG synthesis / HS-GAG biosynthesis / positive regulation of extracellular exosome assembly / HS-GAG degradation ...Defective B3GALT6 causes EDSP2 and SEMDJL1 / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / Defective EXT2 causes exostoses 2 / Defective EXT1 causes exostoses 1, TRPS2 and CHDS / regulation of fibroblast migration / A tetrasaccharide linker sequence is required for GAG synthesis / HS-GAG biosynthesis / positive regulation of extracellular exosome assembly / HS-GAG degradation / inner ear receptor cell stereocilium organization / positive regulation of exosomal secretion / costamere / Respiratory syncytial virus (RSV) attachment and entry / ureteric bud development / Syndecan interactions / RSV-host interactions / thrombospondin receptor activity / positive regulation of focal adhesion assembly / fibronectin binding / negative regulation of T cell proliferation / Retinoid metabolism and transport / positive regulation of stress fiber assembly / lysosomal lumen / neural tube closure / Cell surface interactions at the vascular wall / protein kinase C binding / wound healing / Golgi lumen / cell migration / Attachment and Entry / focal adhesion / cell surface / extracellular exosome / identical protein binding / plasma membrane Similarity search - Function | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model type details | minimized average | ||||||
Authors | Lee, D. / Oh, E.S. / Woods, A. / Couchman, J.R. / Lee, W. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Solution structure of the dimeric cytoplasmic domain of syndecan-4. Authors: Shin, J. / Lee, W. / Lee, D. / Koo, B.K. / Han, I. / Lim, Y. / Woods, A. / Couchman, J.R. / Oh, E.S. #1: Journal: J.Biol.Chem. / Year: 1998 Title: Solution Structure of a Syndecan-4 Cytoplasmic Domain and Its Interaction with Phosphatidylinositol 4,5-Bisphosphate | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ejp.cif.gz | 306.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ejp.ent.gz | 254.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ejp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ejp_validation.pdf.gz | 349 KB | Display | wwPDB validaton report |
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Full document | 1ejp_full_validation.pdf.gz | 471 KB | Display | |
Data in XML | 1ejp_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 1ejp_validation.cif.gz | 34.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/1ejp ftp://data.pdbj.org/pub/pdb/validation_reports/ej/1ejp | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 3314.850 Da / Num. of mol.: 2 / Fragment: WHOLE CYTOPLASMIC DOMAIN / Source method: obtained synthetically Details: This peptide was chemically synthesized. The sequence of this petide occurs naturally in humans (Homo Sapiens). References: UniProt: P31431 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined using standard 2D homonuclear techniques. |
-Sample preparation
Details |
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Sample conditions |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: The structures are based on a total of 306 restraints, 246 are intramonomer NOE-derived distance constraints, 48 intermonomer NOE-derived distance restraints and 12 dihedral angle restraints. | ||||||||||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 90 / Conformers submitted total number: 16 |