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Basic information

Entry
Database: PDB / ID: 3brb
TitleCrystal structure of catalytic domain of the proto-oncogene tyrosine-protein kinase MER in complex with ADP
ComponentsProto-oncogene tyrosine-protein kinase MER
KeywordsTRANSFERASE / ATP-BINDING / DISEASE MUTATION / GLYCOPROTEIN / KINASE / NUCLEOTIDE-BINDING / PHOSPHORYLATION / PROTO-ONCOGENE / RECEPTOR / RETINITIS PIGMENTOSA / SENSORY TRANSDUCTION / TYROSINE-PROTEIN KINASE / VISION / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / Immunoglobulin domain / Membrane / Phosphoprotein / Transmembrane
Function / homology
Function and homology information


negative regulation of leukocyte apoptotic process / negative regulation of lymphocyte activation / neutrophil clearance / natural killer cell differentiation / secretion by cell / negative regulation of cytokine production / vagina development / photoreceptor outer segment / phagocytosis / positive regulation of phagocytosis ...negative regulation of leukocyte apoptotic process / negative regulation of lymphocyte activation / neutrophil clearance / natural killer cell differentiation / secretion by cell / negative regulation of cytokine production / vagina development / photoreceptor outer segment / phagocytosis / positive regulation of phagocytosis / transmembrane receptor protein tyrosine kinase activity / substrate adhesion-dependent cell spreading / cell surface receptor protein tyrosine kinase signaling pathway / Cell surface interactions at the vascular wall / establishment of localization in cell / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / platelet activation / cell migration / nervous system development / cell-cell signaling / retina development in camera-type eye / spermatogenesis / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / cell surface receptor signaling pathway / protein phosphorylation / extracellular space / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Fibronectin type III domain / : / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain ...Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Fibronectin type III domain / : / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Immunoglobulin subtype / Immunoglobulin / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Ig-like domain profile. / Immunoglobulin-like domain / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Immunoglobulin-like domain superfamily / Transferase(Phosphotransferase); domain 1 / 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Tyrosine-protein kinase Mer
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWalker, J.R. / Huang, X. / Finerty Jr, P.J. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: J.Struct.Biol. / Year: 2009
Title: Structural insights into the inhibited states of the Mer receptor tyrosine kinase.
Authors: Huang, X. / Finerty, P. / Walker, J.R. / Butler-Cole, C. / Vedadi, M. / Schapira, M. / Parker, S.A. / Turk, B.E. / Thompson, D.A. / Dhe-Paganon, S.
History
DepositionDec 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proto-oncogene tyrosine-protein kinase MER
B: Proto-oncogene tyrosine-protein kinase MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,95112
Polymers71,7792
Non-polymers1,17210
Water4,179232
1
A: Proto-oncogene tyrosine-protein kinase MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5046
Polymers35,8891
Non-polymers6155
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Proto-oncogene tyrosine-protein kinase MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4476
Polymers35,8891
Non-polymers5585
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.385, 89.880, 69.537
Angle α, β, γ (deg.)90.00, 103.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Proto-oncogene tyrosine-protein kinase MER / C-mer / Receptor tyrosine kinase MerTK


Mass: 35889.434 Da / Num. of mol.: 2 / Fragment: Catalytic domain: Residues 574-864
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Peripheral blood leukocyte / Gene: MERTK, MER / Plasmid: pET28a-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q12866, receptor protein-tyrosine kinase

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Non-polymers , 5 types, 242 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.26 Å3/Da / Density % sol: 45.67 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: MER protein (38 mg/mL) was pre-incubated with 2.5 mM ATP and 10 mM MgCl2 for 3 hours at room temperature. Crystals were obtained at 290K against 29% PEG 400, 0.2M MgCl2, and 0.1 M Tris-HCl ...Details: MER protein (38 mg/mL) was pre-incubated with 2.5 mM ATP and 10 mM MgCl2 for 3 hours at room temperature. Crystals were obtained at 290K against 29% PEG 400, 0.2M MgCl2, and 0.1 M Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9179 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 6, 2007 / Details: Rh coated Si mirrors
RadiationMonochromator: Horizontal bent Si(111), asymmetrically cut with water-cooled Cu block
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 1.9→25.05 Å / Num. all: 49802 / Num. obs: 49802 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rsym value: 0.09 / Net I/σ(I): 24.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2.3929 / Rsym value: 0.659 / % possible all: 88.7

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2P0C

2p0c


Resolution: 1.9→25.05 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.937 / SU B: 8.805 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2487 5 %RANDOM
Rwork0.19221 ---
obs0.19469 47038 98.32 %-
all-49525 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.967 Å2
Baniso -1Baniso -2Baniso -3
1-6.06 Å20 Å20.38 Å2
2---2.51 Å20 Å2
3----3.39 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4126 0 67 232 4425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224361
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.9945917
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.585540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.76123.483178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04715742
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2431529
X-RAY DIFFRACTIONr_chiral_restr0.1030.2672
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023219
X-RAY DIFFRACTIONr_nbd_refined0.2020.21995
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22987
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2248
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.28
X-RAY DIFFRACTIONr_mcbond_it1.90432766
X-RAY DIFFRACTIONr_mcangle_it2.68644322
X-RAY DIFFRACTIONr_scbond_it3.60251834
X-RAY DIFFRACTIONr_scangle_it4.71271595
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 164 -
Rwork0.259 3073 -
obs--87.63 %
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)
13.4725-1.6076-0.47338.99321.33427.2606-0.11760.06740.00530.0930.29550.74210.1052-0.6785-0.1779-0.0494-0.0125-0.00830.19070.09610.1666-11.871626.3438-21.0181
26.24164.7288-0.15115.83381.5433.65360.2351-0.14840.28760.5573-0.09740.7083-0.603-0.4804-0.13770.07070.03920.02870.17620.04020.1237-6.434830.7325-19.5926
367.425421.04425.89426.56811.83970.5153-1.87565.58761.37242.51282.24692.79512.93871.4515-0.37130.605-0.0022-0.00140.6033-0.0020.6083-24.834723.3773-8.6325
48.9464-3.81933.28384.1104-2.11752.97650.0420.13840.12790.1620.01790.3145-0.2581-0.4046-0.05990.01190.02930.02270.0988-0.01470.1107-8.247126.8768-8.1713
52.4342-1.6821-0.9275.39150.56821.11530.07270.19720.1528-0.29790.0191-0.29110.1065-0.0969-0.09170.0656-0.0331-0.0160.16810.00290.09243.332214.3563-18.3288
62.86190.2406-0.41373.05140.5143.1904-0.08020.11420.0660.19580.0846-0.1522-0.05060.114-0.00440.075-0.0276-0.03160.1605-0.00550.14455.455315.7983-3.285
71.0214-0.206-0.17862.90810.59962.19040.005-0.00860.00260.00560.01420.2897-0.0524-0.2194-0.01920.01320.006-0.01430.170.00120.1549-3.04817.8025-5.9486
84.30051.8271.5035.11582.36742.8967-0.02290.246-0.34720.40850.12080.03140.45170.061-0.09790.17510.0018-0.00530.09920.01430.1030.3258-5.9646-2.4297
92.86190.7029-0.22812.39580.44182.75180.0408-0.1069-0.03980.2730.0454-0.16640.06920.1896-0.08620.09480.0112-0.04070.1259-0.01280.07085.667.01425.6912
103.95091.0434-0.16839.13713.42596.9062-0.05130.3481-0.1538-0.6020.27860.4148-0.117-0.7063-0.22720.0442-0.0422-0.05950.17880.07260.1235-12.9456-29.6785-22.1305
112.2201-0.13641.23529.7697-0.5296.8298-0.16510.0250.0162-0.18820.23770.20720.0331-0.2357-0.07260.0755-0.0309-0.02420.17420.03420.1434-7.2384-29.9336-17.8358
125.8324-0.1541.48313.49115.67469.7395-0.32330.645-0.0948-0.6948-0.25660.7397-1.0756-0.1570.57990.01490.0555-0.16020.07460.03990.1063-18.1249-25.2328-35.2775
138.76863.55933.97622.83450.41142.84360.03170.3616-0.3815-0.28480.0783-0.01770.4225-0.2757-0.110.078-0.0232-0.01180.0946-0.04290.06880.4905-28.146-32.1053
145.95330.44952.34673.73733.36283.8832-0.0075-0.0074-0.007-0.0561-0.26890.8843-0.0675-0.82590.2764-0.0803-0.0187-0.04380.21620.0570.157-13.5556-27.2389-24.9995
152.09560.70182.510710.58413.51563.69940.1778-0.22720.03360.77880.1235-0.30470.2634-0.0301-0.30130.03730.0199-0.0080.1361-0.01070.08167.4924-11.7273-12.8102
163.2197-0.07870.63432.84890.05153.9067-0.0076-0.0851-0.0757-0.04610.0868-0.2292-0.08770.145-0.07920.0360.0199-0.0030.1664-0.00940.174411.7713-17.2558-28.1945
171.0453-0.2068-0.22051.96370.41031.85660.07330.05690.0747-0.18130.04470.0366-0.2156-0.0428-0.1180.02350.0206-0.01430.1350.00360.12425.6818-6.1885-31.8932
1811.6290.32530.43083.0038-0.86259.65320.0312-0.90210.13760.8046-0.0291-0.68070.74491.072-0.0021-0.050.0798-0.06530.1973-0.07210.082524.0348-14.51-29.628
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA575 - 60624 - 55
2X-RAY DIFFRACTION2AA607 - 62156 - 70
3X-RAY DIFFRACTION3AA625 - 63574 - 84
4X-RAY DIFFRACTION4AA636 - 65885 - 107
5X-RAY DIFFRACTION5AA666 - 690115 - 139
6X-RAY DIFFRACTION6AA691 - 719140 - 168
7X-RAY DIFFRACTION7AA720 - 805169 - 254
8X-RAY DIFFRACTION8AA806 - 827255 - 276
9X-RAY DIFFRACTION9AA828 - 861277 - 310
10X-RAY DIFFRACTION10BB575 - 59724 - 46
11X-RAY DIFFRACTION11BB598 - 61947 - 68
12X-RAY DIFFRACTION12BB620 - 63569 - 84
13X-RAY DIFFRACTION13BB636 - 65185 - 100
14X-RAY DIFFRACTION14BB652 - 674101 - 123
15X-RAY DIFFRACTION15BB675 - 691124 - 140
16X-RAY DIFFRACTION16BB692 - 719141 - 168
17X-RAY DIFFRACTION17BB720 - 851169 - 300
18X-RAY DIFFRACTION18BB852 - 863301 - 312

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