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- PDB-4k9e: Crystal structure of KIT D4D5 fragment in complex with anti-Kit a... -

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Basic information

Entry
Database: PDB / ID: 4k9e
TitleCrystal structure of KIT D4D5 fragment in complex with anti-Kit antibodies Fab79D
Components
  • Mast/stem cell growth factor receptor Kit
  • heavy chain
  • light chain
KeywordsIMMUNE SYSTEM / receptor tyrosine kinase (RTK) / IgG / Fab
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 / 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 / immature B cell differentiation / melanocyte differentiation / positive regulation of mast cell cytokine production / lymphoid progenitor cell differentiation / germ cell migration / myeloid progenitor cell differentiation / digestive tract development / negative regulation of programmed cell death / embryonic hemopoiesis / lamellipodium assembly / tongue development / megakaryocyte development / Regulation of KIT signaling / pigmentation / stem cell population maintenance / mast cell degranulation / positive regulation of Notch signaling pathway / cytokine binding / negative regulation of reproductive process / negative regulation of developmental process / growth factor binding / somatic stem cell population maintenance / hemopoiesis / T cell differentiation / spermatid development / ectopic germ cell programmed cell death / hematopoietic progenitor cell differentiation / : / response to cadmium ion / 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 / B cell differentiation / erythrocyte differentiation / cell chemotaxis / acrosomal vesicle / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / epithelial cell proliferation / stem cell differentiation / positive regulation of receptor signaling pathway via JAK-STAT / visual learning / Signaling by SCF-KIT / receptor protein-tyrosine kinase / cytoplasmic side of plasma membrane / fibrillar center / cytokine-mediated signaling pathway / positive regulation of DNA-binding transcription factor activity / Constitutive Signaling by Aberrant PI3K in Cancer / male gonad development / cell-cell junction / PIP3 activates AKT signaling / regulation of cell population proliferation / regulation of cell shape / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / actin cytoskeleton organization / RAF/MAP kinase cascade / spermatogenesis / protein tyrosine kinase activity / protease binding / positive regulation of MAPK cascade / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / intracellular signal transduction / positive regulation of cell migration / inflammatory response
Similarity search - Function
Mast/stem cell growth factor receptor / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / 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. ...Mast/stem cell growth factor receptor / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / 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 / Immunoglobulins / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Mast/stem cell growth factor receptor Kit
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsResheynyak, A.V. / Boggon, T.J. / Lax, I. / Schlessinger, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural basis for KIT receptor tyrosine kinase inhibition by antibodies targeting the D4 membrane-proximal region.
Authors: Reshetnyak, A.V. / Nelson, B. / Shi, X. / Boggon, T.J. / Pavlenco, A. / Mandel-Bausch, E.M. / Tome, F. / Suzuki, Y. / Sidhu, S.S. / Lax, I. / Schlessinger, J.
History
DepositionApr 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: light chain
H: heavy chain
C: Mast/stem cell growth factor receptor Kit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7464
Polymers72,5253
Non-polymers2211
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-27 kcal/mol
Surface area29660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.577, 94.577, 320.876
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Antibody light chain


Mass: 24940.662 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody heavy chain


Mass: 23539.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Protein Mast/stem cell growth factor receptor Kit / SCFR / Piebald trait protein / PBT / Proto-oncogene c-Kit / Tyrosine-protein kinase Kit / p145 c- ...SCFR / Piebald trait protein / PBT / Proto-oncogene c-Kit / Tyrosine-protein kinase Kit / p145 c-kit / v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog


Mass: 24044.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIT, SCFR / Production host: unidentified baculovirus
References: UniProt: P10721, receptor protein-tyrosine kinase
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.86 Å3/Da / Density % sol: 56.93 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.2
Details: 20-24% PEG 400, 0.1 M Tris-HCl, pH 8.2, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 18, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 24161 / Num. obs: 24161 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Rsym value: 0.086 / Net I/σ(I): 10.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.7-2.85.20.518189.8
2.8-2.916.60.5199.2
2.91-3.0480.419199.7
3.04-3.28.50.282199.8
3.2-3.48.40.182199.8
3.4-3.668.50.116199.9
3.66-4.038.50.087199.9
4.03-4.628.40.068199.9
4.62-5.818.20.0661100
5.81-507.70.04199.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→44.779 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.34 / σ(F): 1.35 / Phase error: 25.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2823 1138 5.17 %
Rwork0.2467 --
obs0.2484 22010 90.82 %
all-22010 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.4151 Å2
Refinement stepCycle: LAST / Resolution: 2.7→44.779 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4856 0 14 79 4949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044991
X-RAY DIFFRACTIONf_angle_d0.7566786
X-RAY DIFFRACTIONf_dihedral_angle_d13.0461757
X-RAY DIFFRACTIONf_chiral_restr0.051767
X-RAY DIFFRACTIONf_plane_restr0.003865
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.8280.4389420.3279783X-RAY DIFFRACTION28
2.828-2.9770.35471590.33922709X-RAY DIFFRACTION97
2.977-3.16350.36021640.31252796X-RAY DIFFRACTION100
3.1635-3.40770.28941400.27232825X-RAY DIFFRACTION100
3.4077-3.75050.2631580.24112828X-RAY DIFFRACTION100
3.7505-4.29280.27521730.21672868X-RAY DIFFRACTION100
4.2928-5.4070.19721430.19672927X-RAY DIFFRACTION100
5.407-44.78540.29231590.23683136X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
16.45960.3192-0.00071.33380.76495.341-0.58810.7494-0.0422-0.66650.4357-0.1669-0.62581.13290.16450.8197-0.2589-0.00580.6409-0.03520.308918.107-11.8473-30.7038
24.33341.2034-0.961.9578-0.54715.3318-0.415-0.086-0.2824-0.32780.1743-0.11130.7636-0.33970.17470.41940.01850.16390.34540.0320.436353.42011.3519-28.1874
36.53173.1131.86322.83310.33723.807-0.342-0.2402-0.2646-0.14340.0734-0.1553-0.43560.62230.17060.2494-0.019-0.03360.3529-0.0230.243918.4475-12.0358-7.988
43.20441.9061-0.5012.1110.11070.0151-0.2548-0.24660.6571-0.69070.2387-0.11610.46490.4978-0.0270.3265-0.03280.08770.5683-0.03890.3935.6408-0.0001-16.25
52.38930.929-0.16752.7828-1.58115.3985-0.0975-0.51470.3314-0.2015-0.0999-0.3654-0.1677-0.63080.05450.18430.04950.02260.6246-0.01450.423344.0389.6489-16.8604
66.1962.76571.59293.4060.42424.8965-0.5541-0.16150.3858-0.3410.18460.149-0.0148-0.36660.1590.32060.0641-0.09540.1848-0.15170.3409-3.4668-20.7219-16.0686
70.411-0.8375-0.69073.93210.19471.20450.23040.0274-0.0397-0.163-0.04280.2782-0.3259-0.0361-0.20250.22510.1011-0.11730.6514-0.1970.427-11.05965.3649-7.9446
85.02050.63460.50346.0354-2.07915.42290.14710.41330.06720.31720.15920.4816-0.17380.3564-0.39420.43780.14750.01850.7609-0.10450.298-12.654917.4675-6.7019
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN L AND (RESID 2:109)
2X-RAY DIFFRACTION2CHAIN L AND (RESID 110:227)
3X-RAY DIFFRACTION3CHAIN H AND (RESID 0:100)
4X-RAY DIFFRACTION4CHAIN H AND (RESID 101:138)
5X-RAY DIFFRACTION5CHAIN H AND (RESID 139:219)
6X-RAY DIFFRACTION6CHAIN C AND (RESID 311:387)
7X-RAY DIFFRACTION7CHAIN C AND (RESID 388:457)
8X-RAY DIFFRACTION8CHAIN C AND (RESID 458:509)

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