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- PDB-1obx: Crystal structure of the complex of PDZ2 of syntenin with an inte... -

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Basic information

Entry
Database: PDB / ID: 1obx
TitleCrystal structure of the complex of PDZ2 of syntenin with an interleukin 5 receptor alpha peptide.
Components
  • INTERLEUKIN 5 RECEPTOR ALPHA
  • SYNTENIN 1
KeywordsCELL ADHESION / ADHESION-COMPLEX / PDZ DOMAIN / SIGNAL TRANSDUCTION / NUCLEAR PROTEIN
Function / homology
Function and homology information


interleukin-5 receptor activity / regulation of interleukin-5 production / 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 ...interleukin-5 receptor activity / regulation of interleukin-5 production / 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 / interleukin-5-mediated signaling pathway / positive regulation of exosomal secretion / positive regulation of leukocyte proliferation / negative regulation of receptor internalization / inflammatory response to antigenic stimulus / frizzled binding / cytokine receptor activity / protein targeting to membrane / Ephrin signaling / RIPK1-mediated regulated necrosis / growth factor binding / positive regulation of transforming growth factor beta receptor signaling pathway / cytokine binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / Interleukin receptor SHC signaling / 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 / cytokine-mediated signaling pathway / Regulation of necroptotic cell death / azurophil granule lumen / melanosome / extracellular vesicle / presynapse / actin cytoskeleton organization / RAF/MAP kinase cascade / positive regulation of cell growth / chemical synaptic transmission / nuclear membrane / blood microparticle / Ras protein signal transduction / cytoskeleton / receptor complex / intracellular signal transduction / positive regulation of cell migration / membrane raft / protein heterodimerization activity / external side of plasma membrane / 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 / signal transduction / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Short hematopoietin receptor, family 2, conserved site / Short hematopoietin receptor family 2 signature. / Type I cytokine receptor, cytokine-binding domain / : / Interleukin-6 receptor alpha chain, binding / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. ...Short hematopoietin receptor, family 2, conserved site / Short hematopoietin receptor family 2 signature. / Type I cytokine receptor, cytokine-binding domain / : / Interleukin-6 receptor alpha chain, binding / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Roll / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
: / Syntenin-1 / Interleukin-5 receptor subunit alpha
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsKang, B.S. / Cooper, D.R. / Devedjiev, Y. / Derewenda, U. / Derewenda, Z.S.
CitationJournal: Structure / Year: 2003
Title: Molecular Roots of Degenerate Specificity in Syntenin'S Pdz2 Domain: Reassessment of the Pdz Recognition Paradigm
Authors: Kang, B.S. / Cooper, D.R. / Devedjiev, Y. / Derewenda, U. / Derewenda, Z.S.
History
DepositionJan 31, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SYNTENIN 1
B: INTERLEUKIN 5 RECEPTOR ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6446
Polymers9,3342
Non-polymers3104
Water2,594144
1
A: SYNTENIN 1
B: INTERLEUKIN 5 RECEPTOR ALPHA
hetero molecules

A: SYNTENIN 1
B: INTERLEUKIN 5 RECEPTOR ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,28712
Polymers18,6674
Non-polymers6208
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)53.723, 55.978, 51.094
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2004-

HOH

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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 / TACIP18 / PRO-TGF-ALPHA CYTOPLASMIC DOMAIN-INTERACTING PROTEIN 18


Mass: 8394.598 Da / Num. of mol.: 1 / Fragment: PDZ2, RESIDUES 197-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O00560
#2: Protein/peptide INTERLEUKIN 5 RECEPTOR ALPHA / IL-5R-ALPHA / CD125 ANTIGEN


Mass: 938.975 Da / Num. of mol.: 1 / Fragment: LAST 8 RESIDUES, RESIDUES 413-420 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q01344
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMOL_ID 1: FUNCTIONS AS AN ADAPTER PROTEIN. MAY ALSO FUNCTION TO COUPLE SYNDECANS TO CYTOSKELETAL ...MOL_ID 1: FUNCTIONS AS AN ADAPTER PROTEIN. MAY ALSO FUNCTION TO COUPLE SYNDECANS TO CYTOSKELETAL TRANSCRIPTION PROTEINS OR SIGNALING COMPONENTS. ALSO SEEMS TO COUPLE FACTOR SOX4 TO THE IL-5 RECEPTOR (IL5RA) (MOL_ID 2 IN THIS ENTRY)

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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: 2.4 Å3/Da / Density % sol: 38.1 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7
Details: SITTING DROP 0.1 M HEPES, PH 7.0, 1.6 M AMMONIUM SULFATE, 20 MM COCL2, 0.2 M MGSO4 WITH MICROSEEDIN
Crystal grow
*PLUS
Temperature: 294 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1 MHEPES1reservoirpH7.0
21.6 Mammonium sulfate1reservoir
320 mM1reservoirCoCl2
40.2 M1reservoirMgSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97946
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 29, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.25→20 Å / Num. obs: 155256 / % possible obs: 95.7 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.0051 / Net I/σ(I): 33.5
Reflection shellResolution: 1.25→1.29 Å / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2.15 / % possible all: 75
Reflection
*PLUS
Highest resolution: 1.25 Å / Lowest resolution: 20 Å / Num. measured all: 20850 / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
% possible obs: 75 % / Num. unique obs: 1611 / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2.15

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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: 1.35→19.39 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 0.922 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.212 848 5 %RANDOM
Rwork0.176 ---
obs0.177 16170 98.5 %-
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: 20.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.35→19.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms586 0 12 144 742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021598
X-RAY DIFFRACTIONr_bond_other_d0.0010.02546
X-RAY DIFFRACTIONr_angle_refined_deg2.0941.953805
X-RAY DIFFRACTIONr_angle_other_deg0.93331274
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.256576
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_restr0.1470.2101
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02645
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02105
X-RAY DIFFRACTIONr_nbd_refined0.1990.2113
X-RAY DIFFRACTIONr_nbd_other0.2420.2662
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0870.2358
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.277
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3450.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3020.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3571.5383
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.5042622
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.1363215
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.744.5183
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: 1.35→1.39 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.305 67
Rwork0.212 1150
Refinement
*PLUS
Num. reflection obs: 16171
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.13

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