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- PDB-5g1d: The complex structure of syntenin-1 PDZ domain with c-terminal ex... -

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Basic information

Entry
Database: PDB / ID: 5g1d
TitleThe complex structure of syntenin-1 PDZ domain with c-terminal extension
Components
  • SYNDECAN-4
  • SYNTENIN-1
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


A tetrasaccharide linker sequence is required for GAG synthesis / HS-GAG biosynthesis / HS-GAG degradation / Cell surface interactions at the vascular wall / Neurofascin interactions / RIPK1-mediated regulated necrosis / Syndecan interactions / Regulation of necroptotic cell death / Ephrin signaling / Retinoid metabolism and transport ...A tetrasaccharide linker sequence is required for GAG synthesis / HS-GAG biosynthesis / HS-GAG degradation / Cell surface interactions at the vascular wall / Neurofascin interactions / RIPK1-mediated regulated necrosis / Syndecan interactions / Regulation of necroptotic cell death / Ephrin signaling / Retinoid metabolism and transport / regulation of fibroblast migration / interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / inner ear receptor cell stereocilium organization / neurexin family protein binding / syndecan binding / presynapse assembly / costamere / positive regulation of exosomal secretion / negative regulation of receptor internalization / frizzled binding / ureteric bud development / Neutrophil degranulation / thrombospondin receptor activity / positive regulation of transforming growth factor beta receptor signaling pathway / regulation of mitotic cell cycle / growth factor binding / positive regulation of focal adhesion assembly / fibronectin binding / positive regulation of epithelial to mesenchymal transition / positive regulation of protein kinase activity / positive regulation of phosphorylation / negative regulation of T cell proliferation / positive regulation of stress fiber assembly / ionotropic glutamate receptor binding / phosphatidylinositol-4,5-bisphosphate binding / cell adhesion molecule binding / ephrin receptor binding / protein sequestering activity / protein kinase C binding / neural tube closure / adherens junction / wound healing / melanosome / cell migration / presynapse / cell-cell signaling / positive regulation of cell growth / nuclear membrane / Ras protein signal transduction / cytoskeleton / cell adhesion / positive regulation of cell migration / membrane raft / protein heterodimerization activity / focal adhesion / positive regulation of cell population proliferation / protein-containing complex binding / endoplasmic reticulum membrane / negative regulation of transcription by RNA polymerase II / cell surface / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / plasma membrane / cytosol / cytoplasm
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 / PDZ domain / Pdz3 Domain / PDZ domain ...Syndecan / Syndecan, conserved site / Syndecans signature. / Syndecan/Neurexin domain / Syndecan domain / Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Syndecan-4 / Syntenin-1
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsLee, I. / Kim, H. / Yun, J.H. / Lee, W.
CitationJournal: Sci.Rep. / Year: 2016
Title: New Structural Insight of C-Terminal Region of Syntenin-1, Enhancing the Molecular Dimerization and Inhibitory Function Related on Syndecan-4 Signaling.
Authors: Choi, Y. / Yun, J.H. / Yoo, J. / Kim, H. / Lee, I. / Son, H.N. / Kim, I.S. / Yoon, H.S. / Zimmermann, P. / Couchman, J.R. / Cho, H.S. / Oh, E.S. / Lee, W.
History
DepositionMar 25, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Other
Revision 1.2Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SYNTENIN-1
B: SYNTENIN-1
C: SYNDECAN-4
D: SYNDECAN-4


Theoretical massNumber of molelcules
Total (without water)45,4734
Polymers45,4734
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-19.9 kcal/mol
Surface area17270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.525, 88.529, 90.368
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SYNTENIN-1 / / SYNDECAN-BINDING PROTEIN 1


Mass: 21824.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PET21B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9JI92
#2: Protein/peptide SYNDECAN-4 /


Mass: 911.954 Da / Num. of mol.: 2 / Fragment: 195-202 / Source method: obtained synthetically / Source: (synth.) RATTUS NORVEGICUS (Norway rat) / References: UniProt: P34901*PLUS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.49 % / Description: NONE
Crystal growDetails: 0.2 M LITHIUM SULFATE MONOHYDRATE, 0.1 M TRIS HYDROCHLORIDE (PH 8.5), 30% (W/V) POLYETHYLENE GLYCOL 4000

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97952
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97952 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 13799 / % possible obs: 97.6 % / Observed criterion σ(I): 0.2 / Redundancy: 8.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 24
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 4.36 / % possible all: 93.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.81→50 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.896 / SU B: 23.016 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R Free: 0.314 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23493 667 5 %RANDOM
Rwork0.19426 ---
obs0.19624 12615 96.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.641 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2---0.39 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 2.81→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2687 0 0 0 2687
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0222735
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2691.9423683
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6955345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.01924.407118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.06315494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.781516
X-RAY DIFFRACTIONr_chiral_restr0.1420.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021998
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.21149
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3420.21916
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.290
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1380.218
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0570.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.341.51772
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.61822786
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.67731040
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.2314.5897
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.805→2.878 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 47 -
Rwork0.231 781 -
obs--83.22 %

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