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- PDB-4ckj: Crystal structure of RET tyrosine kinase domain bound to adenosine -

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Basic information

Entry
Database: PDB / ID: 4ckj
TitleCrystal structure of RET tyrosine kinase domain bound to adenosine
ComponentsPROTO-ONCOGENE TYROSINE-PROTEIN KINASE RECEPTOR RET
KeywordsTRANSFERASE
Function / homology
Function and homology information


Peyer's patch morphogenesis / positive regulation of metanephric glomerulus development / posterior midgut development / ureter maturation / embryonic epithelial tube formation / glial cell-derived neurotrophic factor receptor signaling pathway / lymphocyte migration into lymphoid organs / membrane protein proteolysis / positive regulation of peptidyl-serine phosphorylation of STAT protein / Formation of the ureteric bud ...Peyer's patch morphogenesis / positive regulation of metanephric glomerulus development / posterior midgut development / ureter maturation / embryonic epithelial tube formation / glial cell-derived neurotrophic factor receptor signaling pathway / lymphocyte migration into lymphoid organs / membrane protein proteolysis / positive regulation of peptidyl-serine phosphorylation of STAT protein / Formation of the ureteric bud / positive regulation of neuron maturation / Formation of the nephric duct / enteric nervous system development / neuron cell-cell adhesion / innervation / plasma membrane protein complex / neuron maturation / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of cell adhesion mediated by integrin / neural crest cell migration / ureteric bud development / response to pain / regulation of axonogenesis / homophilic cell adhesion via plasma membrane adhesion molecules / positive regulation of cell size / RET signaling / regulation of cell adhesion / cellular response to retinoic acid / NPAS4 regulates expression of target genes / transmembrane receptor protein tyrosine kinase activity / axon guidance / receptor protein-tyrosine kinase / positive regulation of neuron projection development / activation of cysteine-type endopeptidase activity involved in apoptotic process / MAPK cascade / retina development in camera-type eye / signaling receptor activity / RAF/MAP kinase cascade / protein tyrosine kinase activity / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / early endosome / receptor complex / endosome membrane / positive regulation of cell migration / response to xenobiotic stimulus / axon / protein phosphorylation / neuronal cell body / calcium ion binding / dendrite / positive regulation of gene expression / positive regulation of DNA-templated transcription / signal transduction / ATP binding / plasma membrane
Similarity search - Function
Tyrosine-protein kinase, Ret receptor / Tyrosine-protein kinase receptor Ret, cadherin like domain 3 / Ret, cadherin like domain 1 / RET, cadherin-like domain 4 / RET Cadherin like domain 1 / RET Cadherin like domain 3 / RET Cadherin like domain 4 / Cadherin domain / Cadherins domain profile. / Cadherin-like ...Tyrosine-protein kinase, Ret receptor / Tyrosine-protein kinase receptor Ret, cadherin like domain 3 / Ret, cadherin like domain 1 / RET, cadherin-like domain 4 / RET Cadherin like domain 1 / RET Cadherin like domain 3 / RET Cadherin like domain 4 / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / 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 / Phosphorylase Kinase; domain 1 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / 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 / FORMIC ACID / Proto-oncogene tyrosine-protein kinase receptor Ret
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsPlaza-Menacho, I. / Barnouin, K. / Goodman, K. / Martinez-Torres, R.J. / Borg, A. / Murray-Rust, J. / Mouilleron, S. / Knowles, P. / McDonald, N.Q.
CitationJournal: Mol. Cell / Year: 2014
Title: Oncogenic RET kinase domain mutations perturb the autophosphorylation trajectory by enhancing substrate presentation in trans.
Authors: Plaza-Menacho, I. / Barnouin, K. / Goodman, K. / Martinez-Torres, R.J. / Borg, A. / Murray-Rust, J. / Mouilleron, S. / Knowles, P. / McDonald, N.Q.
History
DepositionJan 6, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references / Other
Revision 1.2Feb 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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 RECEPTOR RET
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,79218
Polymers35,7881
Non-polymers1,00417
Water1,928107
1
A: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE RECEPTOR RET
hetero molecules

A: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE RECEPTOR RET
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,58436
Polymers71,5762
Non-polymers2,00734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area9370 Å2
ΔGint-11.7 kcal/mol
Surface area23500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.190, 69.090, 78.640
Angle α, β, γ (deg.)90.00, 101.76, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-3000-

HOH

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Components

#1: Protein PROTO-ONCOGENE TYROSINE-PROTEIN KINASE RECEPTOR RET / CADHERIN FAMILY MEMBER 12 / PROTO-ONCOGENE C-RET


Mass: 35788.215 Da / Num. of mol.: 1 / Fragment: RESIDUES 705-1013
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: P07949, receptor protein-tyrosine kinase
#2: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN TERMINAL RESIDUES GPLSL ARE VECTOR DERIVES RESIDUES.

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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: 2.72 Å3/Da / Density % sol: 54.77 % / Description: NONE
Crystal growpH: 5.5 / Details: pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.65→40 Å / Num. obs: 46229 / % possible obs: 90.8 % / Observed criterion σ(I): 1.2 / Redundancy: 1.8 % / Biso Wilson estimate: 27.19 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 4.8
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.2 / % possible all: 91

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IVT

2ivt


Resolution: 1.65→49.736 Å / SU ML: 0.18 / σ(F): 1.35 / Phase error: 18.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1811 2090 5 %
Rwork0.1533 --
obs0.1547 41491 89.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.4 Å2
Refinement stepCycle: LAST / Resolution: 1.65→49.736 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2293 0 67 107 2467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.022540
X-RAY DIFFRACTIONf_angle_d1.8383437
X-RAY DIFFRACTIONf_dihedral_angle_d15.03958
X-RAY DIFFRACTIONf_chiral_restr0.115378
X-RAY DIFFRACTIONf_plane_restr0.01433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.68840.33061500.26832608X-RAY DIFFRACTION89
1.6884-1.73060.29221310.25032637X-RAY DIFFRACTION90
1.7306-1.77740.25821540.21412666X-RAY DIFFRACTION92
1.7774-1.82970.22931420.18882691X-RAY DIFFRACTION92
1.8297-1.88880.23781300.17452588X-RAY DIFFRACTION89
1.8888-1.95630.20441440.15372611X-RAY DIFFRACTION90
1.9563-2.03460.19361460.13842630X-RAY DIFFRACTION90
2.0346-2.12720.1721260.13622572X-RAY DIFFRACTION88
2.1272-2.23940.18371330.1372609X-RAY DIFFRACTION89
2.2394-2.37970.15471340.14552568X-RAY DIFFRACTION87
2.3797-2.56340.18261410.14292632X-RAY DIFFRACTION90
2.5634-2.82130.20191440.15412656X-RAY DIFFRACTION91
2.8213-3.22950.19411260.14332645X-RAY DIFFRACTION90
3.2295-4.06860.14441590.14372631X-RAY DIFFRACTION90
4.0686-49.75820.17291300.1572657X-RAY DIFFRACTION88
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)
10.7812-1.0751-0.56771.74480.69810.4238-0.0430.1811-0.0873-0.03250.03580.25680.037-0.1170.01360.15720.0042-0.00250.1639-0.00170.263218.76323.43782.7365
21.425-0.43160.12521.0594-0.28051.6314-0.0762-0.07870.18930.1374-0.04260.1489-0.2644-0.03310.04060.24460.032-0.0040.1636-0.02310.217224.0669.425314.6998
31.6255-0.5368-0.46060.98120.40271.4471-0.0831-0.3991-0.15190.19210.0013-0.0058-0.06820.1194-0.00520.22190.0132-0.00780.24580.03790.148836.8849-1.530420.8626
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 700 THROUGH 781 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 782 THROUGH 847 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 848 THROUGH 1013 )

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