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- PDB-2o27: Structure of a class III RTK signaling assembly -

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Basic information

Entry
Database: PDB / ID: 2o27
TitleStructure of a class III RTK signaling assembly
ComponentsKit ligand
KeywordsCYTOKINE / SIGNALING PROTEIN / stem cell factor / receptor tyrosine kinase / class III / receptor-ligand complex / growth factor / 4-helix bundle
Function / homology
Function and homology information


positive regulation of myeloid leukocyte differentiation / stem cell factor receptor binding / mast cell migration / positive regulation of hematopoietic progenitor cell differentiation / Regulation of KIT signaling / negative regulation of mast cell apoptotic process / positive regulation of hematopoietic stem cell proliferation / melanocyte migration / Signaling by SCF-KIT / myeloid leukocyte differentiation ...positive regulation of myeloid leukocyte differentiation / stem cell factor receptor binding / mast cell migration / positive regulation of hematopoietic progenitor cell differentiation / Regulation of KIT signaling / negative regulation of mast cell apoptotic process / positive regulation of hematopoietic stem cell proliferation / melanocyte migration / Signaling by SCF-KIT / myeloid leukocyte differentiation / positive regulation of melanocyte differentiation / positive regulation of mast cell proliferation / mast cell apoptotic process / RAF/MAP kinase cascade / mast cell proliferation / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of Ras protein signal transduction / neural crest cell migration / positive regulation of leukocyte migration / embryonic hemopoiesis / germ cell development / ectopic germ cell programmed cell death / hematopoietic progenitor cell differentiation / T cell proliferation / positive regulation of T cell proliferation / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / filopodium / cytokine activity / growth factor activity / response to organic cyclic compound / male gonad development / positive regulation of peptidyl-tyrosine phosphorylation / lamellipodium / cell population proliferation / Ras protein signal transduction / cytoskeleton / cell adhesion / apoptotic process / positive regulation of cell population proliferation / negative regulation of apoptotic process / extracellular space / extracellular region / membrane / plasma membrane / cytoplasm
Similarity search - Function
Stem cell factor / Stem cell factor / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLiu, H. / Chen, X. / Focia, P. / 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: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kit ligand
B: Kit ligand


Theoretical massNumber of molelcules
Total (without water)32,8902
Polymers32,8902
Non-polymers00
Water8,647480
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-5 kcal/mol
Surface area14490 Å2
MethodPISA
2
A: Kit ligand

B: Kit ligand


Theoretical massNumber of molelcules
Total (without water)32,8902
Polymers32,8902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555y,-x+y,z+1/61
Buried area1940 Å2
ΔGint-11 kcal/mol
Surface area14080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.270, 43.270, 248.433
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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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.: 2 / Fragment: residues 28-166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kitlg, Kitl, Mgf, Sl, Slf / Plasmid: pGEX-4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P20826
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / 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: 2.04 Å3/Da / Density % sol: 39.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.8M ammonium sulfate, 0.1M Hepes, pH pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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: Dec 15, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 13625 / Num. obs: 13625 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 43.5
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 13 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 5 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2O26

2o26


Resolution: 2.2→18.74 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 158204.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.266 646 5.1 %RANDOM
Rwork0.242 ---
obs0.242 12636 95.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 132.484 Å2 / ksol: 0.305536 e/Å3
Displacement parametersBiso mean: 56.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.91 Å21.01 Å20 Å2
2--1.91 Å20 Å2
3----3.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.2→18.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1987 0 0 480 2467
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.01
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: 2.2→2.34 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.302 104 5.1 %
Rwork0.256 1927 -
obs--91.7 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3carbohydrate.param
X-RAY DIFFRACTION4ion.param

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