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- PDB-2hmh: Crystal structure of SOCS3 in complex with gp130(pTyr757) phospho... -

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Basic information

Entry
Database: PDB / ID: 2hmh
TitleCrystal structure of SOCS3 in complex with gp130(pTyr757) phosphopeptide.
Components
  • Interleukin-6 receptor beta chain
  • Suppressor of cytokine signaling 3
KeywordsCytokine Regulator / Socs3 / gp130 / pTyr / peptide complex
Function / homology
Function and homology information


Regulation of IFNG signaling / PTK6 Activates STAT3 / oncostatin-M receptor activity / IL-6-type cytokine receptor ligand interactions / leukemia inhibitory factor receptor activity / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / Interferon gamma signaling / Interleukin-27 signaling / triglyceride mobilization ...Regulation of IFNG signaling / PTK6 Activates STAT3 / oncostatin-M receptor activity / IL-6-type cytokine receptor ligand interactions / leukemia inhibitory factor receptor activity / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / Interferon gamma signaling / Interleukin-27 signaling / triglyceride mobilization / interleukin-6 receptor activity / interleukin-6 binding / Interleukin-6 signaling / Interleukin-35 Signalling / Interferon alpha/beta signaling / oncostatin-M receptor complex / ciliary neurotrophic factor receptor binding / Inactivation of CSF3 (G-CSF) signaling / ciliary neurotrophic factor receptor complex / interleukin-27-mediated signaling pathway / interleukin-6 receptor complex / negative regulation of tyrosine phosphorylation of STAT protein / regulation of Notch signaling pathway / interleukin-6 receptor binding / branching involved in labyrinthine layer morphogenesis / interleukin-11-mediated signaling pathway / cellular response to interleukin-17 / placenta blood vessel development / Neddylation / positive regulation of astrocyte differentiation / Antigen processing: Ubiquitination & Proteasome degradation / intestinal epithelial cell development / 1-phosphatidylinositol-3-kinase regulator activity / protein tyrosine kinase inhibitor activity / phosphatidylinositol 3-kinase complex / cytokine receptor activity / miRNA binding / glycogen metabolic process / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / protein tyrosine kinase activator activity / negative regulation of cytosolic calcium ion concentration / neuronal cell body membrane / positive regulation of smooth muscle cell migration / cytokine binding / phosphatidylinositol phosphate biosynthetic process / cell surface receptor signaling pathway via JAK-STAT / positive regulation of osteoblast differentiation / negative regulation of signal transduction / coreceptor activity / positive regulation of T cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / negative regulation of insulin receptor signaling pathway / phosphotyrosine residue binding / cellular response to leukemia inhibitory factor / positive regulation of cell differentiation / regulation of protein phosphorylation / cytokine-mediated signaling pathway / negative regulation of inflammatory response / cytoplasmic side of plasma membrane / cell body / scaffold protein binding / negative regulation of neuron apoptotic process / cell differentiation / receptor complex / intracellular signal transduction / protein ubiquitination / membrane raft / external side of plasma membrane / neuronal cell body / dendrite / positive regulation of cell population proliferation / signal transduction / identical protein binding / cytosol
Similarity search - Function
Suppressor of cytokine signalling 3 / SOCS3, SH2 domain / suppressors of cytokine signalling / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / Type I cytokine receptor, cytokine-binding domain / Interleukin-6 receptor alpha chain, binding / Immunoglobulin C2-set-like, ligand-binding ...Suppressor of cytokine signalling 3 / SOCS3, SH2 domain / suppressors of cytokine signalling / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / Type I cytokine receptor, cytokine-binding domain / Interleukin-6 receptor alpha chain, binding / Immunoglobulin C2-set-like, ligand-binding / Ig-like C2-type domain / Long hematopoietin receptor, Gp130 family 2, conserved site / Long hematopoietin receptor, gp130 family signature. / : / SH2 domain / SHC Adaptor Protein / Fibronectin type III domain / Fibronectin type 3 domain / SH2 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Immunoglobulin-like fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Suppressor of cytokine signaling 3 / Interleukin-6 receptor subunit beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBergamin, E. / Wu, J. / Hubbard, S.R.
CitationJournal: Structure / Year: 2006
Title: Structural basis for phosphotyrosine recognition by suppressor of cytokine signaling-3.
Authors: Bergamin, E. / Wu, J. / Hubbard, S.R.
History
DepositionJul 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Aug 30, 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_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Suppressor of cytokine signaling 3
B: Interleukin-6 receptor beta chain


Theoretical massNumber of molelcules
Total (without water)18,3322
Polymers18,3322
Non-polymers00
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-13 kcal/mol
Surface area7540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.918, 94.708, 69.922
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Suppressor of cytokine signaling 3 / SOCS-3 / Cytokine-inducible SH2 protein 3 / CIS-3 / Protein EF-10


Mass: 17043.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Socs3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O35718
#2: Protein/peptide Interleukin-6 receptor beta chain / IL-6R-beta / Interleukin 6 signal transducer / Membrane glycoprotein 130 / gp130 / CD130 antigen


Mass: 1289.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in mice. / References: UniProt: Q00560
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 1.94 Å3/Da / Density % sol: 36.49 %
Crystal growTemperature: 297 K / pH: 6.5
Details: 30% PEG8000, 0.1 M Sodium Cacodylate, 0.2 M Sodium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 297K, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.00551
DetectorDate: Mar 11, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00551 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 9956 / % possible obs: 99.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.56 / Net I/σ(I): 15.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.323 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 2SHP

2shp


Resolution: 2→47.35 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.887 / SU B: 5.401 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.291 470 4.7 %RANDOM
Rwork0.242 ---
obs0.244 9442 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20 Å2
2---0.41 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 2→47.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1051 0 0 58 1109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221074
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.9771457
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9995128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.63623.19147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.51715172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.421157
X-RAY DIFFRACTIONr_chiral_restr0.0830.2163
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02803
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.2447
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2713
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.265
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.225
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9281.5677
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.61921067
X-RAY DIFFRACTIONr_scbond_it1.833452
X-RAY DIFFRACTIONr_scangle_it2.7694.5390
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 37 -
Rwork0.272 678 -
obs--99.31 %

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