[English] 日本語
Yorodumi
- PDB-2vif: Crystal structure of SOCS6 SH2 domain in complex with a c-KIT pho... -

+
Open data


ID or keywords:

Loading...

-
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 / stem cell factor receptor activity / hematopoietic stem cell migration / melanocyte adhesion / positive regulation of pyloric antrum smooth muscle contraction / positive regulation of colon smooth muscle contraction / erythropoietin-mediated signaling pathway / positive regulation of vascular associated smooth muscle cell differentiation / melanocyte migration / positive regulation of dendritic cell cytokine production / Kit signaling pathway / regulation of bile acid metabolic process / positive regulation of small intestine smooth muscle contraction / mast cell differentiation / positive regulation of mast cell proliferation / mast cell chemotaxis / Fc receptor signaling pathway / glycosphingolipid metabolic process / negative regulation of T cell activation / mast cell proliferation / positive regulation of long-term neuronal synaptic plasticity / detection of mechanical stimulus involved in sensory perception of sound / positive regulation of pseudopodium assembly / positive regulation of mast cell cytokine production / immature B cell differentiation / melanocyte differentiation / germ cell migration / lymphoid progenitor cell differentiation / 1-phosphatidylinositol-3-kinase regulator activity / myeloid progenitor cell differentiation / digestive tract development / negative regulation of programmed cell death / phosphatidylinositol 3-kinase complex / regulation of growth / embryonic hemopoiesis / lamellipodium assembly / pigmentation / tongue development / megakaryocyte development / Regulation of KIT signaling / mast cell degranulation / stem cell population maintenance / positive regulation of Notch signaling pathway / cytokine binding / negative regulation of reproductive process / negative regulation of developmental process / spermatid development / growth factor binding / somatic stem cell population maintenance / cell surface receptor signaling pathway via JAK-STAT / phosphatidylinositol phosphate biosynthetic process / hemopoiesis / immunological synapse / T cell differentiation / ectopic germ cell programmed cell death / hematopoietic progenitor cell differentiation / positive regulation of phospholipase C activity / response to cadmium ion / negative regulation of signal transduction / ovarian follicle development / positive regulation of tyrosine phosphorylation of STAT protein / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transmembrane receptor protein tyrosine kinase activity / SH2 domain binding / cell chemotaxis / post-translational protein modification / B cell differentiation / erythrocyte differentiation / acrosomal vesicle / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / epithelial cell proliferation / proteasomal protein catabolic process / stem cell differentiation / positive regulation of receptor signaling pathway via JAK-STAT / visual learning / defense response / Signaling by SCF-KIT / cytoplasmic side of plasma membrane / receptor protein-tyrosine kinase / fibrillar center / cytokine-mediated signaling pathway / male gonad development / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of DNA-binding transcription factor activity / cell-cell junction / PIP3 activates AKT signaling / Neddylation / regulation of cell population proliferation / regulation of cell shape / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling
Similarity search - Function
Suppressor of cytokine signalling 6 / SOCS6, SH2 domain / SOCS6, SOCS box domain / suppressors of cytokine signalling / SOCS box / Mast/stem cell growth factor receptor / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box ...Suppressor of cytokine signalling 6 / SOCS6, SH2 domain / SOCS6, SOCS box domain / suppressors of cytokine signalling / SOCS box / Mast/stem cell growth factor receptor / SOCS box-like domain superfamily / SOCS box domain / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Ethylene glycol


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more