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- PDB-6ith: Structure of the transmembrane domain of syndecan 2 in micelles -

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Basic information

Entry
Database: PDB / ID: 6ith
TitleStructure of the transmembrane domain of syndecan 2 in micelles
ComponentsSyndecan-2
KeywordsMEMBRANE PROTEIN / DPC / micelles
Function / homology
Function and homology information


protein metabolic process => GO:0019538 / Defective B3GALT6 causes EDSP2 and SEMDJL1 / glycosaminoglycan catabolic process / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / Defective EXT2 causes exostoses 2 / Defective EXT1 causes exostoses 1, TRPS2 and CHDS / A tetrasaccharide linker sequence is required for GAG synthesis / HS-GAG biosynthesis / glycosaminoglycan biosynthetic process ...protein metabolic process => GO:0019538 / Defective B3GALT6 causes EDSP2 and SEMDJL1 / glycosaminoglycan catabolic process / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / Defective EXT2 causes exostoses 2 / Defective EXT1 causes exostoses 1, TRPS2 and CHDS / A tetrasaccharide linker sequence is required for GAG synthesis / HS-GAG biosynthesis / glycosaminoglycan biosynthetic process / HS-GAG degradation / dendrite morphogenesis / retinoid metabolic process / Syndecan interactions / regulation of dendrite morphogenesis / leukocyte migration / ephrin receptor signaling pathway / Retinoid metabolism and transport / EPHB-mediated forward signaling / lysosomal lumen / post-translational protein modification / PDZ domain binding / Post-translational protein phosphorylation / Cell surface interactions at the vascular wall / Golgi lumen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cell migration / collagen-containing extracellular matrix / membrane => GO:0016020 / endoplasmic reticulum lumen / cell surface / identical protein binding / plasma membrane
Similarity search - Function
Syndecan-2 / 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
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLi, Q. / Ng, H.Q. / Kang, C.
CitationJournal: FEBS Lett. / Year: 2019
Title: Secondary structure and topology of the transmembrane domain of Syndecan-2 in detergent micelles.
Authors: Li, Q. / Ng, H.Q. / Kang, C.
History
DepositionNov 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Syndecan-2


Theoretical massNumber of molelcules
Total (without water)4,7161
Polymers4,7161
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3850 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Syndecan-2 / / SYND2 / Fibroglycan / Heparan sulfate proteoglycan core protein / HSPG


Mass: 4715.657 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SDC2, HSPG1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P34741

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic2NOESY
121isotropic23D HN(CA)CB
131isotropic22D 1H-15N HSQC
141isotropic12D 1H-15N HSQC
151isotropic23D HNCO
161isotropic2HN(CO)CACB
171isotropic23D HNCA
181isotropic23D HBHA(CO)NH
192isotropic12D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
micelle120 mM sodium phosphate, 5 % w/v DPC, 1 mM DTT, 0.5 mM [U-100% 13C; U-100% 15N] SCN2, 90% H2O/10% D2O20 mM Sodium phosphate, pH6.5, 5% DPC and 1 mM DTT.13C15N90% H2O/10% D2O
micelle220 mM sodium phosphate, 5 % DPC, 1 mM DTT, 0.5 mM [U-99% 15N] SCN2, 100% D2O20 mM Sodium phosphate, pH6.5, 5% DPC and 1 mM DTT in D2O.15N100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium phosphatenatural abundance1
5 % w/vDPCnatural abundance1
1 mMDTTnatural abundance1
0.5 mMSCN2[U-100% 13C; U-100% 15N]1
20 mMsodium phosphatenatural abundance2
5 %DPCnatural abundance2
1 mMDTTnatural abundance2
0.5 mMSCN2[U-99% 15N]2
Sample conditionsDetails: 0.5 mM in 20 mM Sodium phosphate, pH6.5, 5% DPC and 1 mM DTT.
Ionic strength: 20 mM / Ionic strength err: 0.2 / Label: 13C15N / pH: 6.5 / PH err: 0.1 / Pressure: AMBIENT atm / Temperature: 313 K / Temperature err: 0.1

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE7002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
NMRView3.97Johnson, One Moon Scientificchemical shift assignment
AUREMOLBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 15

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