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- PDB-1ejq: SOLUTION STRUCTURE OF THE SYNDECAN-4 WHOLE CYTOPLASMIC DOMAIN IN ... -

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Entry
Database: PDB / ID: 1ejq
TitleSOLUTION STRUCTURE OF THE SYNDECAN-4 WHOLE CYTOPLASMIC DOMAIN IN THE PRESENCE OF PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE
ComponentsSYNDECAN-4
KeywordsSIGNALING PROTEIN / Symmetric dimer / complexed with PIP2
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 / HS-GAG degradation / positive regulation of extracellular exosome assembly ...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 / HS-GAG degradation / positive regulation of extracellular exosome assembly / inner ear receptor cell stereocilium organization / positive regulation of exosomal secretion / costamere / ureteric bud development / Syndecan 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 / protein kinase C binding / Cell surface interactions at the vascular wall / wound healing / Golgi lumen / cell migration / Attachment and Entry / focal adhesion / cell surface / extracellular exosome / identical protein binding / plasma membrane
Similarity search - Function
Syndecan / Syndecan, conserved site / Syndecans signature. / Syndecan/Neurexin domain / Syndecan domain / Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif
Similarity search - Domain/homology
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsShin, J. / Oh, E.S. / Lee, D. / Couchman, J.R. / Lee, W.
CitationJournal: To be Published
Title: SOLUTION STRUCTURE OF THE SYNDECAN-4 WHOLE CYTOPLASMIC DOMAIN IN THE PRESENCE OF PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE
Authors: Shin, J. / Oh, E.S. / Lee, D. / Couchman, J.R. / Lee, W.
History
DepositionMar 4, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 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 (RESIDUES 171-198) / 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
3332D NOESY
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 cytoplasmic domain;Molar ratio of 4:1(syndecan-4 peptide:PIP2);50mM sodium phosphate;90% H2O 10% D2O90% H2O/10% D2O
22-4mM Syndecan-4 cytoplasmic domain;Molar ratio of 4:1(syndecan-4 peptide:PIP2);50mM sodium phosphate;90% H2O 10% D2O90% H2O/10% D2O
32-4mM Syndecan-4 cytoplasmic domain;Molar ratio of 4:1(syndecan-4 peptide:PIP2);50mM sodium phosphate;90% H2O 10% D2O100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150mM sodium phosphate 7.4 1 atm298 K
250mM sodium phosphate 7.4 1 atm298 K
350mM sodium phosphate 7.4 1 atm298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX5002
Bruker DRXBrukerDRX5003

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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
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 90 / Conformers submitted total number: 15

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