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- PDB-2p0c: Catalytic Domain of the Proto-oncogene Tyrosine-protein Kinase MER -

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Basic information

Entry
Database: PDB / ID: 2p0c
TitleCatalytic Domain of the Proto-oncogene Tyrosine-protein Kinase MER
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
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 / positive regulation of phagocytosis / 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 / positive regulation of phagocytosis / phagocytosis / transmembrane receptor protein tyrosine kinase activity / substrate adhesion-dependent cell spreading / phosphatidylinositol 3-kinase/protein kinase B signal transduction / establishment of localization in cell / Cell surface interactions at the vascular wall / receptor protein-tyrosine kinase / platelet activation / cell surface receptor protein tyrosine kinase signaling pathway / cell migration / retina development in camera-type eye / cell-cell signaling / nervous system development / spermatogenesis / cell surface receptor signaling pathway / receptor complex / 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 / Tyrosine 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. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Ig-like domain profile. / Immunoglobulin-like domain / Phosphorylase Kinase; domain 1 / Immunoglobulin-like domain superfamily / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / BETA-MERCAPTOETHANOL / Tyrosine-protein kinase Mer
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWalker, J.R. / Huang, X. / Finerty Jr., P.J. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
Citation
Journal: 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.
#1: Journal: Cell Growth Differ. / Year: 1994
Title: Cloning and mRNA expression analysis of a novel human protooncogene, c-mer.
Authors: Graham, D.K. / Dawson, T.L. / Mullaney, D.L. / Snodgrass, H.R. / Earp, H.S.
#2: Journal: Cell Growth Differ. / Year: 1994
Title: Erratum
Authors: Graham, D.K. / Dawson, T.L. / Mullaney, D.L. / Snodgrass, H.R. / Earp, H.S.
#3: Journal: Nat.Genet. / Year: 2000
Title: Mutations in MERTK, the human orthologue of the RCS rat retinal dystrophy gene, cause retinitis pigmentosa.
Authors: Gal, A. / Li, Y. / Thompson, D.A. / Weir, J. / Orth, U. / Jacobson, S.G. / Apfelstedt-Sylla, E. / Vollrath, D.
History
DepositionFeb 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 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 ...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.pdbx_leaving_atom_flag / _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

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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)72,9428
Polymers71,7792
Non-polymers1,1636
Water2,954164
1
A: Proto-oncogene tyrosine-protein kinase MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4984
Polymers35,8891
Non-polymers6093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Proto-oncogene tyrosine-protein kinase MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4444
Polymers35,8891
Non-polymers5553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.470, 90.057, 69.253
Angle α, β, γ (deg.)90.00, 102.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Peripheral blood leukocyte / Gene: MERTK, MER / Production host: Escherichia coli (E. coli)
References: UniProt: Q12866, receptor protein-tyrosine kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.23 Å3/Da / Density % sol: 44.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: The protein in 20mM Tris-HCl pH 8.0, 0.5M NaCl, 5% glycerol, 2mM BME, 2.5 mM AMP-PNP, 10 mM MgCl2, 5mM peptide (ADEPNYETWG) was mixed with crystallization buffer (15% PEG 8000, 0.2M ammonium ...Details: The protein in 20mM Tris-HCl pH 8.0, 0.5M NaCl, 5% glycerol, 2mM BME, 2.5 mM AMP-PNP, 10 mM MgCl2, 5mM peptide (ADEPNYETWG) was mixed with crystallization buffer (15% PEG 8000, 0.2M ammonium sulfate, and 0.1 M Sodium cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 23, 2007
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. all: 24544 / Num. obs: 24544 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rsym value: 0.067 / Net I/σ(I): 21.6
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 5.2 / Num. unique all: 2456 / Rsym value: 0.293 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2G15

2g15


Resolution: 2.4→24.79 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.88 / SU B: 14.05 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.398 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27392 1232 5 %RANDOM
Rwork0.20414 ---
obs0.20761 23326 99.54 %-
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: 39.11 Å2
Baniso -1Baniso -2Baniso -3
1-5.72 Å20 Å2-0.91 Å2
2---3.14 Å20 Å2
3----2.97 Å2
Refinement stepCycle: LAST / Resolution: 2.4→24.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3934 0 69 164 4167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224105
X-RAY DIFFRACTIONr_angle_refined_deg1.2011.9975564
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1945490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.74223.663172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.86215710
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.831525
X-RAY DIFFRACTIONr_chiral_restr0.0730.2631
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022982
X-RAY DIFFRACTIONr_nbd_refined0.1950.21912
X-RAY DIFFRACTIONr_nbtor_refined0.2990.22771
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2214
X-RAY DIFFRACTIONr_metal_ion_refined0.160.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.26
X-RAY DIFFRACTIONr_mcbond_it0.76622564
X-RAY DIFFRACTIONr_mcangle_it1.31633994
X-RAY DIFFRACTIONr_scbond_it1.61841790
X-RAY DIFFRACTIONr_scangle_it2.17451570
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 84 -
Rwork0.211 1705 -
obs--99.39 %
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)
117.5494-10.8724-5.383119.60410.62635.7825-0.69180.08680.8026-0.1919-0.08831.30610.267-1.07720.7801-0.07140.27880.13510.17760.14310.3518-15.762133.2925-16.3338
25.40946.47770.922828.59950.85848.17360.3191-0.0539-0.0509-0.37050.07381.0031-0.0443-0.7464-0.3929-0.08770.0495-0.03730.15470.11340.1154-8.889325.441-20.636
327.5313-5.27218.48763.3877-0.71364.9127-0.19280.0263-0.01210.42340.19790.1637-0.4894-0.3161-0.00510.15480.06780.02690.02330.06670.0408-8.030926.0822-5.4855
44.8913-4.9821-0.22367.33930.39560.26480.02650.2599-0.1119-0.04160.07390.17070.2054-0.2747-0.10040.0627-0.02420.04780.16930.03450.0349-3.177619.43-16.8623
514.71425.033112.34838.298811.191217.7434-0.27541.1250.5408-0.50830.6025-0.59980.14852.1409-0.3270.0586-0.22970.16180.4066-0.11580.200114.94837.7541-17.5927
60.49120.1389-0.27012.84420.08681.7180.0352-0.03270.03020.20230.01360.1532-0.0529-0.0804-0.04880.05170.0150.03240.1142-0.00050.0744-1.490210.8967-4.1927
77.11232.1938-0.12366.39542.51125.1142-0.26230.1786-0.54520.4616-0.00890.44650.6255-0.5250.27120.1557-0.04190.051-0.03420.00860.0925-4.4094-7.4728-3.4005
83.33011.5013-0.15292.34220.96333.19430.03830.0708-0.13970.46240.1734-0.27590.31260.1033-0.21170.11980.0396-0.01580.0778-0.00050.05216.7066.01984.6702
94.68160.03910.27397.741-0.11954.7789-0.13240.3527-0.1420.12680.26891.06540.523-0.5669-0.13650.0746-0.0732-0.00270.15440.04260.0917-10.3336-30.6855-20.634
1014.15373.1213.37225.1501-0.81684.7361-0.2520.0836-0.3551-0.44430.3456-0.11810.7799-0.3282-0.09360.2096-0.10640.03960.0854-0.00660.0527-2.2409-27.842-32.5419
111.43583.4741.90889.01724.17122.8652-0.0335-0.0710.06620.06680.19870.1276-0.0583-0.2268-0.16520.01890.0197-0.030.16190.04090.0969-0.6275-19.3017-18.0085
122.89530.47482.54762.71442.60285.6244-0.06470.0625-0.12950.20690.3102-0.07090.3440.4929-0.24550.0040.0275-0.01210.1762-0.01350.099212.9548-16.1113-26.0495
130.76340.0944-1.1582.80210.742.3444-0.05680.1201-0.04470.06730.09890.30750.1189-0.3596-0.0421-0.0485-0.0195-0.0530.17980.00520.13431.1725-15.7877-28.8752
140.50830.4642-0.46013.06250.89421.0714-0.04580.05010.0571-0.2690.06450.2293-0.2673-0.1062-0.01860.04920.0346-0.00310.17130.01830.11313.1763-4.8154-31.6396
1510.2778-0.7903-0.30174.87970.86462.994-0.0414-0.05630.8075-0.7650.07370.2392-0.4576-0.3154-0.03230.1950.0718-0.0005-0.0150.03310.05652.36995.4275-33.3083
163.2995-2.30980.1133.2741-0.41513.30590.08070.00880.0824-0.26320.2722-0.3028-0.3340.3171-0.35290.01-0.01560.09420.141-0.03780.099815.4718-7.689-35.1417
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA575 - 58924 - 38
2X-RAY DIFFRACTION2AA590 - 63339 - 82
3X-RAY DIFFRACTION3AA634 - 65183 - 100
4X-RAY DIFFRACTION4AA652 - 686101 - 135
5X-RAY DIFFRACTION5AA687 - 697136 - 146
6X-RAY DIFFRACTION6AA698 - 802147 - 251
7X-RAY DIFFRACTION7AA803 - 822252 - 271
8X-RAY DIFFRACTION8AA823 - 861272 - 310
9X-RAY DIFFRACTION9BB575 - 62124 - 70
10X-RAY DIFFRACTION10BB633 - 65182 - 100
11X-RAY DIFFRACTION11BB652 - 690101 - 139
12X-RAY DIFFRACTION12BB691 - 716140 - 165
13X-RAY DIFFRACTION13BB717 - 769166 - 218
14X-RAY DIFFRACTION14BB770 - 805219 - 254
15X-RAY DIFFRACTION15BB806 - 822255 - 271
16X-RAY DIFFRACTION16BB823 - 861272 - 310

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