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- PDB-2vif: Crystal structure of SOCS6 SH2 domain in complex with a c-KIT pho... -

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Basic information

Entry
Database: PDB / ID: 2vif
TitleCrystal structure of SOCS6 SH2 domain in complex with a c-KIT phosphopeptide
Components
  • MAST/STEM CELL GROWTH FACTOR RECEPTOR
  • SUPPRESSOR OF CYTOKINE SIGNALLING 6
KeywordsSIGNALING PROTEIN / GROWTH REGULATION / SIGNAL TRANSDUCTION INHIBITOR / KIT REGULATOR / PHOSPHOTYROSINE
Function / homology
Function and homology information


Dasatinib-resistant KIT mutants / Imatinib-resistant KIT mutants / KIT mutants bind TKIs / Masitinib-resistant KIT mutants / Nilotinib-resistant KIT mutants / Regorafenib-resistant KIT mutants / Signaling by kinase domain mutants of KIT / Sunitinib-resistant KIT mutants / Signaling by juxtamembrane domain KIT mutants / Sorafenib-resistant KIT mutants ...Dasatinib-resistant KIT mutants / Imatinib-resistant KIT mutants / KIT mutants bind TKIs / Masitinib-resistant KIT mutants / Nilotinib-resistant KIT mutants / Regorafenib-resistant KIT mutants / Signaling by kinase domain mutants of KIT / Sunitinib-resistant KIT mutants / Signaling by juxtamembrane domain KIT mutants / Sorafenib-resistant KIT mutants / Signaling by extracellular domain mutants of KIT / hematopoietic stem cell migration / melanocyte adhesion / positive regulation of pyloric antrum smooth muscle contraction / positive regulation of colon smooth muscle contraction / stem cell factor receptor activity / positive regulation of vascular associated smooth muscle cell differentiation / melanocyte migration / Kit signaling pathway / tongue development / : / positive regulation of small intestine smooth muscle contraction / positive regulation of dendritic cell cytokine production / mast cell chemotaxis / positive regulation of mast cell proliferation / mast cell differentiation / Fc receptor signaling pathway / glycosphingolipid metabolic process / mast cell proliferation / positive regulation of pseudopodium assembly / positive regulation of long-term neuronal synaptic plasticity / positive regulation of mast cell cytokine production / negative regulation of T cell activation / lymphoid progenitor cell differentiation / detection of mechanical stimulus involved in sensory perception of sound / melanocyte differentiation / immature B cell differentiation / germ cell migration / erythropoietin-mediated signaling pathway / myeloid progenitor cell differentiation / regulation of growth / digestive tract development / negative regulation of programmed cell death / embryonic hemopoiesis / lamellipodium assembly / positive regulation of tyrosine phosphorylation of STAT protein / Regulation of KIT signaling / megakaryocyte development / growth factor binding / mast cell degranulation / stem cell population maintenance / pigmentation / positive regulation of Notch signaling pathway / cytokine binding / negative regulation of reproductive process / negative regulation of developmental process / hemopoiesis / T cell differentiation / immunological synapse / somatic stem cell population maintenance / spermatid development / cell surface receptor signaling pathway via JAK-STAT / ectopic germ cell programmed cell death / response to cadmium ion / negative regulation of signal transduction / hematopoietic progenitor cell differentiation / positive regulation of DNA-binding transcription factor activity / proteasomal protein catabolic process / ovarian follicle development / signaling adaptor activity / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transmembrane receptor protein tyrosine kinase activity / Negative regulation of FLT3 / Transcriptional and post-translational regulation of MITF-M expression and activity / acrosomal vesicle / SH2 domain binding / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / B cell differentiation / epithelial cell proliferation / erythrocyte differentiation / cell chemotaxis / positive regulation of receptor signaling pathway via JAK-STAT / stem cell differentiation / Signaling by SCF-KIT / defense response / receptor protein-tyrosine kinase / visual learning / cytoplasmic side of plasma membrane / male gonad development / fibrillar center / cytokine-mediated signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / cell-cell junction / cell migration / PIP3 activates AKT signaling / regulation of cell shape / regulation of cell population proliferation / Neddylation / protein autophosphorylation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling
Similarity search - Function
SOCS6, SH2 domain / SOCS6, SOCS box domain / suppressors of cytokine signalling / SOCS box / SOCS box-like domain superfamily / SOCS box domain / Mast/stem cell growth factor receptor / SOCS box domain profile. / SOCS_box / Tyrosine-protein kinase, receptor class III, conserved site ...SOCS6, SH2 domain / SOCS6, SOCS box domain / suppressors of cytokine signalling / SOCS box / SOCS box-like domain superfamily / SOCS box domain / Mast/stem cell growth factor receptor / SOCS box domain profile. / SOCS_box / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / SH2 domain / SHC Adaptor Protein / Immunoglobulin / Immunoglobulin domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Suppressor of cytokine signaling 6 / Mast/stem cell growth factor receptor Kit
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsBullock, A. / Pike, A.C.W. / Savitsky, P. / Keates, T. / Pilka, E.S. / von Delft, F. / Edwards, A. / Weigelt, J. / Arrowsmith, C.H. / Knapp, S.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural Basis for C-Kit Inhibition by the Suppressor of Cytokine Signaling 6 (Socs6) Ubiquitin Ligase.
Authors: Zadjali, F. / Pike, A.C.W. / Vesterlund, M. / Sun, J. / Wu, C. / Li, S.S. / Ronnstrand, L. / Knapp, S. / Bullock, A. / Flores-Morales, A.
History
DepositionNov 30, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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 / struct_conn / struct_site
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 / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SUPPRESSOR OF CYTOKINE SIGNALLING 6
P: MAST/STEM CELL GROWTH FACTOR RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3303
Polymers17,2682
Non-polymers621
Water2,252125
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-9.4 kcal/mol
Surface area8300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.377, 60.143, 71.367
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 SUPPRESSOR OF CYTOKINE SIGNALLING 6 / SOCS-6 / SUPPRESSOR OF CYTOKINE SIGNALING 4 / SOCS-4 / CYTOKINE-INDUCIBLE SH2 PROTEIN 4 / CIS-4


Mass: 15918.718 Da / Num. of mol.: 1 / Fragment: SH2 DOMAIN, RESIDUES 361-499
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21-ELONGIN / References: UniProt: O14544
#2: Protein/peptide MAST/STEM CELL GROWTH FACTOR RECEPTOR / SCFR / PROTO-ONCOGENE TYROSINE-PROTEIN KINASE KIT / C-KIT / CD117 ANTIGEN


Mass: 1349.297 Da / Num. of mol.: 1 / Fragment: RESIDUES 564-574
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21-ELONGIN / References: UniProt: P10721
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTWO CLONING ARTIFACTS - V368D AND R463G

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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: 2.04 Å3/Da / Density % sol: 39.84 % / Description: NONE
Crystal growpH: 6.5
Details: 0.2M AMMONIUM SULPHATE, 30% PEG5000 MONOMETHYLETHER, 0.1M MES PH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98248
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 26, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98248 Å / Relative weight: 1
ReflectionResolution: 1.45→46.03 Å / Num. obs: 23956 / % possible obs: 99.9 % / Redundancy: 4.5 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 10.7
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.704 / Mean I/σ(I) obs: 3 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IZV

2izv


Resolution: 1.45→35.69 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.461 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.198 1210 5.1 %RANDOM
Rwork0.139 ---
obs0.142 22652 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2---0.23 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.45→35.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1118 0 4 125 1247
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211205
X-RAY DIFFRACTIONr_bond_other_d0.0020.02839
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.9511633
X-RAY DIFFRACTIONr_angle_other_deg0.98732025
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3175143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.78822.03459
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.19215201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1031513
X-RAY DIFFRACTIONr_chiral_restr0.0940.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021326
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02274
X-RAY DIFFRACTIONr_nbd_refined0.1890.2206
X-RAY DIFFRACTIONr_nbd_other0.1950.2870
X-RAY DIFFRACTIONr_nbtor_refined0.1850.2568
X-RAY DIFFRACTIONr_nbtor_other0.0840.2631
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.296
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2750.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.8833762
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.01351164
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.6438545
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it9.6411468
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: 1.45→1.49 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.316 73
Rwork0.149 1620

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