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- PDB-4k94: Crystal structure of KIT D4D5 fragment in complex with anti-Kit a... -

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Basic information

Entry
Database: PDB / ID: 4k94
TitleCrystal structure of KIT D4D5 fragment in complex with anti-Kit antibody Fab19
Components
  • Fab19 heavy chain
  • Fab19 light chain
  • Mast/stem cell growth factor receptor Kit
KeywordsIMMUNE SYSTEM / receptor tyrosine kinase (RTK) / Fab / Ig SF
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 / stem cell population maintenance / pigmentation / mast cell degranulation / positive regulation of Notch signaling pathway / negative regulation of reproductive process / negative regulation of developmental process / growth factor binding / cytokine binding / somatic stem cell population maintenance / hemopoiesis / spermatid development / T cell differentiation / Transcriptional and post-translational regulation of MITF-M expression and activity / 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 / cell chemotaxis / acrosomal vesicle / erythrocyte differentiation / 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 / positive regulation of DNA-binding transcription factor activity / cytokine-mediated signaling pathway / 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 / protease binding / protein tyrosine kinase activity / 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
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 ...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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.2Apr 9, 2014Group: Source and taxonomy
Revision 1.3Jul 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

Downloads & links

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Assembly

Deposited unit
L: Fab19 heavy chain
H: Fab19 light chain
C: Mast/stem cell growth factor receptor Kit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2654
Polymers72,0443
Non-polymers2211
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-28 kcal/mol
Surface area28620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.580, 48.980, 106.970
Angle α, β, γ (deg.)90.00, 122.38, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Fab19 heavy chain


Mass: 24603.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Antibody Fab19 light chain


Mass: 23396.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#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 / Plasmid: pFastBac / 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.: 109 / 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: 2.6 Å3/Da / Density % sol: 52.76 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 13% PEG 3350, 0.5 M magnesium chloride, 0.1 M Tris-HCl, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 29794 / Num. obs: 24912 / % possible obs: 84.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rsym value: 0.082 / Net I/σ(I): 11
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.2 / Rsym value: 0.623 / % possible all: 64.1

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→45.495 Å / SU ML: 0.86 / σ(F): 1.36 / Phase error: 25.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2349 1257 5.05 %
Rwork0.198 --
obs0.1998 24910 84.4 %
all-29794 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.527 Å2 / ksol: 0.353 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.3643 Å2-0 Å2-0.0513 Å2
2---1.1882 Å20 Å2
3---1.5524 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45.495 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4690 0 14 109 4813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044827
X-RAY DIFFRACTIONf_angle_d0.776563
X-RAY DIFFRACTIONf_dihedral_angle_d12.2711707
X-RAY DIFFRACTIONf_chiral_restr0.052736
X-RAY DIFFRACTIONf_plane_restr0.003835
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.49520.4024380.3103690X-RAY DIFFRACTION22
2.4952-2.60880.31311000.28281717X-RAY DIFFRACTION56
2.6088-2.74630.34271470.2812588X-RAY DIFFRACTION84
2.7463-2.91830.29871610.25483050X-RAY DIFFRACTION99
2.9183-3.14360.26981470.23623097X-RAY DIFFRACTION99
3.1436-3.45990.24211700.19043073X-RAY DIFFRACTION99
3.4599-3.96030.2091640.17713080X-RAY DIFFRACTION99
3.9603-4.98850.16461610.1473147X-RAY DIFFRACTION100
4.9885-45.50320.24111690.19993211X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.51130.2107-0.59733.89211.33784.05040.0396-0.1128-0.3689-0.2752-0.0491-0.14810.84440.5713-0.05780.38410.1260.03320.22730.01010.224732.4455-12.81189.158
21.5105-0.27660.59011.8871-0.27551.3249-0.1210.57890.3019-1.2616-0.01640.1232-0.1222-0.03090.12311.3983-0.1239-0.27180.50640.03310.355719.8859-0.0173-23.0815
31.1683-0.05240.38812.86160.30914.1428-0.24590.23290.3481-0.53410.25420.3807-0.6634-0.29220.47710.5274-0.0916-0.00160.331-0.11390.200925.75313.058710.0773
40.3140.15330.48111.75271.22433.13580.18880.02170.1134-0.4492-0.12320.0126-0.80430.6592-0.09270.0984-0.18790.1020.3383-0.01640.13732.21918.885918.3986
50.62361.26470.16622.9461-0.15820.78020.0532-0.02190.0107-0.0615-0.0107-0.1281-0.78110.90060.06410.34-0.19090.03430.2597-0.06340.307733.48248.528110.2417
62.32010.3067-0.07553.5999-0.94583.17070.1541-0.2914-0.06520.13170.06640.4609-0.2117-0.0645-0.20750.1-0.0121-0.00270.1847-0.04820.144827.4050.466714.8329
72.6089-0.47531.74342.10070.29622.9984-0.17160.3267-0.0304-1.06830.25670.9534-0.7525-0.1543-0.05570.8121-0.0147-0.24040.22910.07160.637118.203213.7718-11.6307
83.1129-2.32990.35933.36721.64632.29880.30120.0751-0.5411-0.1229-0.36661.2342-0.2802-0.607-0.09450.681-0.0145-0.12140.28980.05960.508714.18146.2619-6.516
97.20233.25531.92054.81670.25463.8965-0.32480.2192-0.1157-0.85060.13641.4129-0.4081-0.6790.22230.60390.0545-0.14980.3756-0.01920.790912.12029.793-10.6556
104.64310.87250.62842.92510.2531.5058-0.0943-0.2232-0.2966-0.09920.0946-0.2890.35460.6108-0.04670.004-0.0357-0.02610.4560.02940.243937.3869-4.318835.7831
112.3301-0.0011-1.26470.918-0.50511.8125-0.04850.01230.39650.56290.23670.2689-0.36460.2566-0.12890.14140.07030.02550.1763-0.01430.188614.6101-4.169546.9054
123.89123.5156-2.4754.277-2.14451.5859-0.23621.1019-0.4788-0.29220.64850.20250.3778-0.4224-0.03450.41430.1179-0.110.4956-0.05430.7014-9.60021.931547.8635
134.1215-3.9183-4.15485.91273.60284.25-0.5958-1.1386-0.370.96830.3906-0.63380.59171.3818-0.10440.32340.07650.05370.53530.21920.610614.1204-3.446249.9036
141.4906-0.7418-2.93162.91410.39257.02110.3265-0.40030.53280.9556-0.04440.5585-0.7062-0.5143-0.19790.330.05910.09120.3146-0.05680.37371.6825-0.573654.2174
159.70430.186-3.44881.52190.61633.45660.3487-0.46440.94010.27590.2950.8111-0.5998-0.8085-0.1330.29080.28810.08260.57110.15780.6575-8.2283-3.890349.6951
169.55150.6545-6.03851.67120.91184.96750.15440.6460.26960.23010.40630.6971-0.5668-1.5164-0.25180.2270.09540.04670.48460.06850.3397-3.3325-7.226646.5259
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN L AND (RESSEQ 3:108)
2X-RAY DIFFRACTION2CHAIN L AND (RESSEQ 109:212)
3X-RAY DIFFRACTION3CHAIN H AND (RESSEQ 1:17)
4X-RAY DIFFRACTION4CHAIN H AND (RESSEQ 18:83)
5X-RAY DIFFRACTION5CHAIN H AND (RESSEQ 84:100)
6X-RAY DIFFRACTION6CHAIN H AND (RESSEQ 101:113)
7X-RAY DIFFRACTION7CHAIN H AND (RESSEQ 114:147)
8X-RAY DIFFRACTION8CHAIN H AND (RESSEQ 148:171)
9X-RAY DIFFRACTION9CHAIN H AND (RESSEQ 172:217)
10X-RAY DIFFRACTION10CHAIN C AND (RESSEQ 310:387)
11X-RAY DIFFRACTION11CHAIN C AND (RESSEQ 388:444)
12X-RAY DIFFRACTION12CHAIN C AND (RESSEQ 445:457)
13X-RAY DIFFRACTION13CHAIN C AND (RESSEQ 458:471)
14X-RAY DIFFRACTION14CHAIN C AND (RESSEQ 472:482)
15X-RAY DIFFRACTION15CHAIN C AND (RESSEQ 483:494)
16X-RAY DIFFRACTION16CHAIN C AND (RESSEQ 495:508)

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