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- PDB-1ejp: SOLUTION STRUCTURE OF THE SYNDECAN-4 WHOLE CYTOPLASMIC DOMAIN -

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Entry
Database: PDB / ID: 1ejp
TitleSOLUTION STRUCTURE OF THE SYNDECAN-4 WHOLE CYTOPLASMIC DOMAIN
ComponentsSYNDECAN-4
KeywordsSIGNALING PROTEIN / symmetric-parallel-interwinded dimer
Function / homology
Function and homology information


Syndecan interactions / A tetrasaccharide linker sequence is required for GAG synthesis / HS-GAG biosynthesis / Cell surface interactions at the vascular wall / HS-GAG degradation / Defective B4GALT7 causes EDS, progeroid type / Defective EXT2 causes exostoses 2 / Retinoid metabolism and transport / Defective EXT1 causes exostoses 1, TRPS2 and CHDS / Defective B3GALT6 causes EDSP2 and SEMDJL1 ...Syndecan interactions / A tetrasaccharide linker sequence is required for GAG synthesis / HS-GAG biosynthesis / Cell surface interactions at the vascular wall / HS-GAG degradation / Defective B4GALT7 causes EDS, progeroid type / Defective EXT2 causes exostoses 2 / Retinoid metabolism and transport / Defective EXT1 causes exostoses 1, TRPS2 and CHDS / Defective B3GALT6 causes EDSP2 and SEMDJL1 / Defective B3GAT3 causes JDSSDHD / regulation of fibroblast migration / positive regulation of extracellular exosome assembly / glycosaminoglycan catabolic process / glycosaminoglycan biosynthetic process / inner ear receptor cell stereocilium organization / positive regulation of exosomal secretion / costamere / ureteric bud development / positive regulation of focal adhesion assembly / fibronectin binding / thrombospondin receptor activity / negative regulation of T cell proliferation / positive regulation of protein kinase activity / positive regulation of stress fiber assembly / neural tube closure / retinoid metabolic process / protein kinase C binding / lysosomal lumen / Golgi lumen / wound healing / cell migration / leukocyte migration / membrane raft / focal adhesion / integral component of plasma membrane / cell surface / extracellular exosome / identical protein binding / plasma membrane
Syndecan/Neurexin domain / Neurexin/syndecan/glycophorin C / Syndecan / Syndecan domain / Syndecans signature. / Syndecan, conserved site
Syndecan-4
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsLee, 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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 3, 2000 / Release: Sep 19, 2001
RevisionDateData content typeGroupProviderType
1.0Sep 19, 2001Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

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Assembly

Deposited unit
A: SYNDECAN-4
B: SYNDECAN-4


Theoretical massNumber of molelcules
Total (without water)6,6302
Polymers6,6302
Non-polymers00
Water0
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)16 / 90structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide SYNDECAN-4 / / AMPHIGLYCAN / RYUDOCAN CORE PROTEIN / SYND4


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

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
222DQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
12-4mM Syndecan-4 peptide ; 50mM phosphate buffer; 90% H2O, 10% D2O90% H2O/10% D2O
22-4mM Syndecan-4 peptide ; 50mM phosphate buffer; 90% H2O, 10% D2O90% H2O/10% D2O
32-4mM Syndecan-4 peptide ; 50mM phosphate buffer; 100% D2O100% D2O
Sample conditions

Ionic strength: 50mM sodium phosphate / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K

Conditions-ID
1
2
3
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XWINNMR2.5Brukercollection
XWINNMR2.5Brukerprocessing
Sparky3.6James, T.data analysis
X-PLOR3.851Brunger, A.Trefinement
RefinementMethod: 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 representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 90 / Conformers submitted total number: 16

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