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- PDB-1v1t: Crystal structure of the PDZ tandem of human syntenin in complex ... -

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Basic information

Entry
Database: PDB / ID: 1v1t
TitleCrystal structure of the PDZ tandem of human syntenin in complex with TNEYKV peptide
Components
  • SYNTENIN 1
  • TNEYKV PEPTIDE
KeywordsCELL ADHESION / ADHESION-COMPLEX / PDZ DOMAIN / SCAFFOLDING PROTEIN
Function / homology
Function and homology information


interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / syndecan binding / Neurofascin interactions / neurexin family protein binding / presynapse assembly / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / positive regulation of exosomal secretion ...interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / syndecan binding / Neurofascin interactions / neurexin family protein binding / presynapse assembly / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / positive regulation of exosomal secretion / negative regulation of receptor internalization / frizzled binding / protein targeting to membrane / Ephrin signaling / RIPK1-mediated regulated necrosis / growth factor binding / positive regulation of transforming growth factor beta receptor signaling pathway / positive regulation of phosphorylation / positive regulation of epithelial to mesenchymal transition / cell adhesion molecule binding / ionotropic glutamate receptor binding / ephrin receptor binding / phosphatidylinositol-4,5-bisphosphate binding / protein sequestering activity / regulation of mitotic cell cycle / adherens junction / positive regulation of JNK cascade / Regulation of necroptotic cell death / azurophil granule lumen / melanosome / extracellular vesicle / presynapse / actin cytoskeleton organization / positive regulation of cell growth / chemical synaptic transmission / nuclear membrane / blood microparticle / Ras protein signal transduction / 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 / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / 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
BENZOIC ACID / Syntenin-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGrembecka, J. / Cierpicki, T. / Devedjiev, Y. / Cooper, D.R. / Derewenda, U. / Derewenda, Z.S.
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
DepositionApr 23, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.3Oct 9, 2019Group: Data collection / Other / Source and taxonomy / Category: pdbx_database_status / pdbx_entity_src_syn / Item: _pdbx_database_status.status_code_sf
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SYNTENIN 1
B: SYNTENIN 1
S: TNEYKV PEPTIDE
T: TNEYKV PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6675
Polymers37,5454
Non-polymers1221
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-16.6 kcal/mol
Surface area16870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.341, 72.341, 125.676
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsPROTEIN CHAINS A AND B FORM A DIMERIC COMPLEX, BUTSINCE EACH OF THESE IS IN COMPLEX WITH A PEPTIDE(CHAINS S AND T), THIS ENTRY HAS BEEN CLASSIFIED AS A TETRAMERIC 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 / Fragment: PDZ TANDEM, RESIDUES 108-273
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: GENE, SDCBP OR MDA9 OR SYCL / Plasmid: PGST-PARALLEL1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O00560
#2: Protein/peptide TNEYKV PEPTIDE


Mass: 753.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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 / pH: 7.5
Details: 20% PEG3350, 0.2M NH4CL, VAPOR DIFFUSION, SITTING DROP, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97912
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 4, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 34079 / % possible obs: 98.7 % / Redundancy: 7 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 19
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 7 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 5.7 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N99

1n99


Resolution: 1.8→63.25 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.895 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.229 993 3.2 %RANDOM
Rwork0.181 ---
obs0.183 30277 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å20 Å2
2---0.53 Å20 Å2
3---1.06 Å2
Refinement stepCycle: LAST / Resolution: 1.8→63.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2576 0 9 281 2866
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212616
X-RAY DIFFRACTIONr_bond_other_d0.0020.022419
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.9543518
X-RAY DIFFRACTIONr_angle_other_deg0.83335653
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8135332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0860.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022888
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02479
X-RAY DIFFRACTIONr_nbd_refined0.2130.2480
X-RAY DIFFRACTIONr_nbd_other0.250.22898
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0820.21689
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2203
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.320.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5041.51660
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.42822679
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.6323956
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.6134.5839
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: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.298 62
Rwork0.193 2232

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