[English] 日本語
Yorodumi
- PDB-3brb: Crystal structure of catalytic domain of the proto-oncogene tyros... -

+
Open data


ID or keywords:

Loading...

-
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 / transmembrane receptor protein tyrosine kinase activity ...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 / transmembrane receptor protein tyrosine kinase activity / substrate adhesion-dependent cell spreading / positive regulation of phagocytosis / cell surface receptor protein tyrosine kinase signaling pathway / Cell surface interactions at the vascular wall / establishment of localization in cell / receptor protein-tyrosine kinase / platelet activation / cell migration / nervous system development / cell-cell signaling / retina development in camera-type eye / spermatogenesis / cell surface receptor signaling pathway / protein phosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / 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. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Ig-like domain profile. / Immunoglobulin-like domain / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more