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- PDB-1ybo: Crystal structure of the PDZ tandem of human syntenin with syndec... -

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Basic information

Entry
Database: PDB / ID: 1ybo
TitleCrystal structure of the PDZ tandem of human syntenin with syndecan peptide
Components
  • Syndecan-4
  • Syntenin 1
KeywordsSTRUCTURAL PROTEIN / PDZ domain / scaffolding protein / adhesion complex
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 / interleukin-5 receptor complex / HS-GAG biosynthesis / interleukin-5 receptor binding ...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 / interleukin-5 receptor complex / HS-GAG biosynthesis / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / inner ear receptor cell stereocilium organization / HS-GAG degradation / syndecan binding / Neurofascin interactions / neurexin family protein binding / presynapse assembly / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / positive regulation of exosomal secretion / costamere / frizzled binding / negative regulation of receptor internalization / protein targeting to membrane / Ephrin signaling / RIPK1-mediated regulated necrosis / ureteric bud development / Syndecan interactions / thrombospondin receptor activity / RSV-host interactions / positive regulation of transforming growth factor beta receptor signaling pathway / growth factor binding / Respiratory syncytial virus (RSV) attachment and entry / fibronectin binding / positive regulation of focal adhesion assembly / positive regulation of phosphorylation / positive regulation of epithelial to mesenchymal transition / Retinoid metabolism and transport / negative regulation of T cell proliferation / cell adhesion molecule binding / positive regulation of stress fiber assembly / ionotropic glutamate receptor binding / ephrin receptor binding / phosphatidylinositol-4,5-bisphosphate binding / protein sequestering activity / lysosomal lumen / regulation of mitotic cell cycle / protein kinase C binding / adherens junction / Cell surface interactions at the vascular wall / neural tube closure / positive regulation of JNK cascade / wound healing / Regulation of necroptotic cell death / Golgi lumen / azurophil granule lumen / cell migration / melanosome / extracellular vesicle / presynapse / actin cytoskeleton organization / positive regulation of cell growth / nuclear membrane / chemical synaptic transmission / blood microparticle / Ras protein signal transduction / Attachment and Entry / cytoskeleton / intracellular signal transduction / positive regulation of cell migration / membrane raft / protein heterodimerization activity / focal adhesion / positive regulation of cell population proliferation / Neutrophil degranulation / endoplasmic reticulum membrane / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / cell surface / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / membrane / 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 ...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
Syntenin-1 / Syndecan-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGrembecka, J. / Cooper, D.R. / Cierpicki, T. / Kang, B.S. / Devedjiev, Y. / Derewenda, Z.
CitationJournal: Biochemistry / Year: 2006
Title: The binding of the PDZ tandem of syntenin to target proteins
Authors: Grembecka, J. / Cierpicki, T. / Devedjiev, Y. / Derewenda, U. / Kang, B.S. / Bushweller, J.H. / Derewenda, Z.S.
History
DepositionDec 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)39,9824
Polymers39,9824
Non-polymers00
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-21 kcal/mol
Surface area16990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.322, 72.322, 125.921
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe dimer in the assymetric unit is the biological assembly

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Components

#1: Protein Syntenin 1 / Syndecan binding protein 1 / Melanoma differentiation associated protein-9 / Mda-9 / Scaffold ...Syndecan binding protein 1 / Melanoma differentiation associated protein-9 / Mda-9 / Scaffold protein Pbp1 / Pro-TGF-alpha cytoplasmic domain-interacting protein 18 / TACIP18


Mass: 18018.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SDCBP, MDA9, SYCL / Plasmid: pGST-parallel-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O00560
#2: Protein/peptide Syndecan-4 / Amphiglycan / SYND4 / Ryudocan core protein


Mass: 1972.329 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: synthesized peptide cooresponding to the C-terminus of syndecan
References: UniProt: P31431
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 49.7 %
Crystal growMethod: vapor diffusion, sitting drop
Details: 20% PEG 3350, 0.2M NH4Cl, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 11, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 23083 / % possible obs: 99 % / Redundancy: 8.3 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.07 / Χ2: 1.388 / Net I/σ(I): 30.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 8.31 / Num. unique all: 2282 / Χ2: 1.208 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.401data extraction
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N99

1n99


Resolution: 2.3→40 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.868 / SU B: 14.26 / SU ML: 0.189 / SU R Cruickshank DPI: 0.403 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.28 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 800 5.2 %RANDOM
Rwork0.193 ---
all0.197 ---
obs-15391 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.247 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å20 Å2
2---0.53 Å20 Å2
3---1.05 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2580 0 0 190 2770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222613
X-RAY DIFFRACTIONr_bond_other_d0.0060.022423
X-RAY DIFFRACTIONr_angle_refined_deg2.6131.9553520
X-RAY DIFFRACTIONr_angle_other_deg1.48435654
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7355333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.27125.089112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.3915482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4341514
X-RAY DIFFRACTIONr_chiral_restr0.0960.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022894
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02490
X-RAY DIFFRACTIONr_nbd_refined0.1940.2460
X-RAY DIFFRACTIONr_nbd_other0.1740.22391
X-RAY DIFFRACTIONr_nbtor_refined0.1590.21192
X-RAY DIFFRACTIONr_nbtor_other0.0850.21562
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2166
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0150.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1180.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2110.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2740.212
X-RAY DIFFRACTIONr_mcbond_it1.0221.52164
X-RAY DIFFRACTIONr_mcbond_other0.0931.5704
X-RAY DIFFRACTIONr_mcangle_it0.92822684
X-RAY DIFFRACTIONr_scbond_it1.47731060
X-RAY DIFFRACTIONr_scangle_it2.2464.5836
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 48 -
Rwork0.184 1068 -
obs--99.91 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.7775-0.51910.55852.1453-0.66672.4920.06570.313-0.23090.1143-0.0476-0.16840.06150.3268-0.0181-0.0785-0.0016-0.0194-0.0349-0.0085-0.07955.77847.16935.105
22.8328-0.9323-0.28462.7674-0.75312.07030.08220.0943-0.0397-0.0777-0.0859-0.08710.056-0.01360.0037-0.01030.02680.0067-0.09710.0143-0.091244.35125.95346.401
32.1351-0.7243-1.01012.43290.33391.50150.06970.0057-0.00270.0243-0.0640.2181-0.06950.0395-0.0058-0.01370.01990.0124-0.1066-0.0067-0.041821.9536.07850.615
43.9619-0.2591-1.18892.1873-0.53831.88890.01620.31370.26280.01590.11780.0973-0.074-0.2518-0.134-0.03930.01390.0297-0.07550.0577-0.048833.27857.50338.446
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA111 - 1954 - 88
22CC1 - 612 - 17
33BB109 - 1952 - 88
44DD3 - 614 - 17

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