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- PDB-4cki: Crystal Structure of oncogenic RET tyrosine kinase M918T bound to... -

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Basic information

Entry
Database: PDB / ID: 4cki
TitleCrystal Structure of oncogenic RET tyrosine kinase M918T bound to adenosine
ComponentsPROTO-ONCOGENE TYROSINE-PROTEIN KINASE RECEPTOR RET
KeywordsTRANSFERASE
Function / homology
Function and homology information


Peyer's patch morphogenesis / GDF15-GFRAL signaling pathway / positive regulation of metanephric glomerulus development / ureter maturation / embryonic epithelial tube formation / glial cell-derived neurotrophic factor receptor signaling pathway / lymphocyte migration into lymphoid organs / posterior midgut development / membrane protein proteolysis / Formation of the ureteric bud ...Peyer's patch morphogenesis / GDF15-GFRAL signaling pathway / positive regulation of metanephric glomerulus development / ureter maturation / embryonic epithelial tube formation / glial cell-derived neurotrophic factor receptor signaling pathway / lymphocyte migration into lymphoid organs / posterior midgut development / membrane protein proteolysis / Formation of the ureteric bud / positive regulation of neuron maturation / neuron cell-cell adhesion / Formation of the nephric duct / enteric nervous system development / 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 / regulation of axonogenesis / response to pain / homophilic cell adhesion via plasma membrane adhesion molecules / RET signaling / positive regulation of cell size / regulation of cell adhesion / cellular response to retinoic acid / transmembrane receptor protein tyrosine kinase activity / NPAS4 regulates expression of target genes / axon guidance / cell surface receptor protein tyrosine kinase signaling pathway / 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 / positive regulation of neuron projection development / MAPK cascade / signaling receptor activity / retina development in camera-type eye / RAF/MAP kinase cascade / protein tyrosine kinase activity / early endosome / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / positive regulation of MAPK cascade / endosome membrane / positive regulation of cell migration / protein phosphorylation / response to xenobiotic stimulus / axon / neuronal cell body / dendrite / calcium ion binding / 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 / RET, Cysteine Rich Domain / Cadherin domain ...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 / RET, Cysteine Rich Domain / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily / : / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / 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 / 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: 2.116 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 / Structure summary
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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)36,47410
Polymers35,8381
Non-polymers6359
Water3,927218
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)72,94720
Polymers71,6762
Non-polymers1,27118
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area6530 Å2
ΔGint-9.4 kcal/mol
Surface area24910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.893, 70.569, 78.997
Angle α, β, γ (deg.)90.00, 101.15, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 35838.098 Da / Num. of mol.: 1 / Fragment: RESIDUES 705-1013 / Mutation: YES
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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 2.74 Å3/Da / Density % sol: 55.16 % / Description: NONE
Crystal growpH: 5.5 / Details: 2M NA FORMATE, 0.1M NA CITRATE, PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.97945
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 26, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.11→40 Å / Num. obs: 22084 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Biso Wilson estimate: 27.73 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.4
Reflection shellResolution: 2.11→2.21 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 2.6 / % possible all: 99

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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: 2.116→39.559 Å / SU ML: 0.2 / σ(F): 0.73 / Phase error: 17.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1905 1107 5 %
Rwork0.156 --
obs0.1577 22078 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.1 Å2
Refinement stepCycle: LAST / Resolution: 2.116→39.559 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2335 0 43 218 2596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052558
X-RAY DIFFRACTIONf_angle_d0.9013473
X-RAY DIFFRACTIONf_dihedral_angle_d13.215990
X-RAY DIFFRACTIONf_chiral_restr0.062382
X-RAY DIFFRACTIONf_plane_restr0.004436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1164-2.21270.25411310.19072487X-RAY DIFFRACTION96
2.2127-2.32930.22371340.16962636X-RAY DIFFRACTION100
2.3293-2.47530.21131700.16562590X-RAY DIFFRACTION100
2.4753-2.66630.2171420.17232628X-RAY DIFFRACTION100
2.6663-2.93460.22121330.17422644X-RAY DIFFRACTION100
2.9346-3.3590.20721260.16732641X-RAY DIFFRACTION100
3.359-4.23120.15861320.13162648X-RAY DIFFRACTION100
4.2312-39.56540.15681390.14332697X-RAY DIFFRACTION100
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)
11.4576-2.5064-0.95214.28681.60260.7837-0.01740.1334-0.3244-0.0391-0.12790.46740.0265-0.26170.10920.1762-0.0111-0.02190.2523-0.00830.316151.7698-1.29070.7197
22.3162-3.3762-0.49415.36290.86140.429-0.11020.0078-0.01470.10890.16170.1355-0.013-0.0438-0.07250.0991-0.0062-0.01860.1466-0.01120.19754.58351.93914.8392
32.475-0.27410.3781.68650.053.3061-0.1939-0.37780.19040.20870.04460.0749-0.3638-0.08520.13510.19650.06010.01570.1787-0.03160.161161.82533.551918.7682
41.7432-0.3243-0.47831.96440.93333.3221-0.0773-0.3757-0.10990.24570.0363-0.07510.03580.30840.00720.16760.0162-0.01190.23420.05880.157575.4996-6.068620.8974
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 700 THROUGH 735 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 736 THROUGH 781 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 782 THROUGH 890 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 891 THROUGH 1013 )

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