[English] 日本語
Yorodumi
- PDB-2o26: Structure of a class III RTK signaling assembly -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2o26
TitleStructure of a class III RTK signaling assembly
Components
  • Kit ligand
  • Mast/stem cell growth factor receptor
KeywordsCYTOKINE/SIGNALING PROTEIN / stem cell factor / receptor tyrosine kinase / class III / receptor-ligand complex / growth factor / cytokine / 4-helix bundle / CYTOKINE-SIGNALING PROTEIN COMPLEX
Function / homology
Function and homology information


glycosphingolipid metabolic process / hematopoietic stem cell migration / positive regulation of melanocyte differentiation / stem cell factor receptor binding / Regulation of KIT signaling / Signaling by SCF-KIT / melanocyte adhesion / positive regulation of pyloric antrum smooth muscle contraction / positive regulation of colon smooth muscle contraction / melanocyte migration ...glycosphingolipid metabolic process / hematopoietic stem cell migration / positive regulation of melanocyte differentiation / stem cell factor receptor binding / Regulation of KIT signaling / Signaling by SCF-KIT / melanocyte adhesion / positive regulation of pyloric antrum smooth muscle contraction / positive regulation of colon smooth muscle contraction / melanocyte migration / stem cell factor receptor activity / positive regulation of vascular associated smooth muscle cell differentiation / Kit signaling pathway / developmental pigmentation / myeloid leukocyte differentiation / Transcriptional and post-translational regulation of MITF-M expression and activity / positive regulation of dendritic cell cytokine production / tongue development / positive regulation of small intestine smooth muscle contraction / positive regulation of mast cell cytokine production / mast cell differentiation / lymphoid progenitor cell differentiation / mast cell chemotaxis / Fc receptor signaling pathway / mast cell proliferation / PIP3 activates AKT signaling / RAF/MAP kinase cascade / immature B cell differentiation / melanocyte differentiation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of long-term neuronal synaptic plasticity / primordial germ cell migration / positive regulation of pseudopodium assembly / myeloid progenitor cell differentiation / detection of mechanical stimulus involved in sensory perception of sound / erythropoietin-mediated signaling pathway / megakaryocyte development / pigmentation / embryonic hemopoiesis / digestive tract development / germ cell development / lamellipodium assembly / somatic stem cell population maintenance / negative regulation of programmed cell death / spermatid development / positive regulation of Notch signaling pathway / positive regulation of tyrosine phosphorylation of STAT protein / growth factor binding / hemopoiesis / positive regulation of MAP kinase activity / cytokine binding / ectopic germ cell programmed cell death / hematopoietic progenitor cell differentiation / T cell differentiation / epithelial cell proliferation / ovarian follicle development / response to cadmium ion / B cell differentiation / transmembrane receptor protein tyrosine kinase activity / peptidyl-tyrosine phosphorylation / male gonad development / acrosomal vesicle / SH2 domain binding / stem cell differentiation / erythrocyte differentiation / cytokine activity / mast cell degranulation / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / cell chemotaxis / filopodium / visual learning / receptor protein-tyrosine kinase / response to radiation / chemotaxis / cytokine-mediated signaling pathway / cytoplasmic side of plasma membrane / fibrillar center / regulation of cell shape / cell-cell junction / protein autophosphorylation / cell migration / lamellipodium / actin cytoskeleton organization / protease binding / protein tyrosine kinase activity / spermatogenesis / cytoskeleton / positive regulation of MAPK cascade / protein phosphorylation / cell differentiation / signaling receptor complex / cell adhesion / intracellular signal transduction / positive regulation of cell migration / inflammatory response / external side of plasma membrane / positive regulation of cell population proliferation / positive regulation of gene expression / cell surface
Similarity search - Function
Stem cell factor / Stem cell factor / Platelet-derived growth factor receptor Ig-like domain 4 / Mast/stem cell growth factor receptor / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Immunoglobulin ...Stem cell factor / Stem cell factor / Platelet-derived growth factor receptor Ig-like domain 4 / Mast/stem cell growth factor receptor / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Immunoglobulin / Immunoglobulin domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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 / Immunoglobulins / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Mast/stem cell growth factor receptor Kit / Kit ligand
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.5 Å
AuthorsLiu, H. / Chen, X. / Focia, P.J. / He, X.
CitationJournal: Embo J. / Year: 2007
Title: Structural basis for stem cell factor-KIT signaling and activation of class III receptor tyrosine kinases.
Authors: Liu, H. / Chen, X. / Focia, P.J. / He, X.
History
DepositionNov 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 2.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Kit ligand
B: Kit ligand
E: Kit ligand
F: Kit ligand
X: Mast/stem cell growth factor receptor
Y: Mast/stem cell growth factor receptor
U: Mast/stem cell growth factor receptor
W: Mast/stem cell growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,50616
Polymers194,8778
Non-polymers4,6288
Water31,1661730
1
A: Kit ligand
B: Kit ligand
X: Mast/stem cell growth factor receptor
Y: Mast/stem cell growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,7538
Polymers97,4394
Non-polymers2,3144
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Kit ligand
F: Kit ligand
U: Mast/stem cell growth factor receptor
W: Mast/stem cell growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,7538
Polymers97,4394
Non-polymers2,3144
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.849, 200.154, 82.023
Angle α, β, γ (deg.)90.00, 91.42, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Kit ligand / C-kit ligand / Stem cell factor / SCF / Mast cell growth factor / MGF / Hematopoietic growth factor ...C-kit ligand / Stem cell factor / SCF / Mast cell growth factor / MGF / Hematopoietic growth factor KL / Steel factor


Mass: 16444.766 Da / Num. of mol.: 4 / Fragment: residues 28-166 / Mutation: N146Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kitlg, Kitl, Mgf, Sl, Slf / Plasmid: pAcGP67A / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P20826
#2: Protein
Mast/stem cell growth factor receptor / SCFR / Proto-oncogene tyrosine-protein kinase Kit / c-kit / CD117 antigen


Mass: 32274.564 Da / Num. of mol.: 4 / Fragment: residues 25-314
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kit, Sl / Plasmid: pGEX-4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P05532, receptor protein-tyrosine kinase
#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1730 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 12, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 82592 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.1
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2.6 / % possible all: 93.3

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.5→19.93 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2913310.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 4155 5 %RANDOM
Rwork0.237 ---
obs0.237 82454 96.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.8781 Å2 / ksol: 0.21433 e/Å3
Displacement parametersBiso mean: 98 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å24.11 Å2
2--15.28 Å20 Å2
3----16.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.76 Å0.7 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13066 0 308 1730 15104
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.417 648 4.9 %
Rwork0.402 12641 -
obs--93.7 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3carbohydrate.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5

+
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