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- PDB-5fm3: Crystal structure of hyper-phosphorylated RET kinase domain with ... -

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Basic information

Entry
Database: PDB / ID: 5fm3
TitleCrystal structure of hyper-phosphorylated RET kinase domain with (proximal) juxtamembrane segment
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
Chem-PP1 / Proto-oncogene tyrosine-protein kinase receptor Ret
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsPlaza-Menacho, I. / Barnouin, K. / Barry, R. / Borg, A. / Orme, M. / Mouilleron, S. / Martinez-Torres, R.J. / Meier, P. / McDonald, N.Q.
CitationJournal: Cell Rep / Year: 2016
Title: RET Functions as a Dual-Specificity Kinase that Requires Allosteric Inputs from Juxtamembrane Elements.
Authors: Plaza-Menacho, I. / Barnouin, K. / Barry, R. / Borg, A. / Orme, M. / Chauhan, R. / Mouilleron, S. / Martinez-Torres, R.J. / Meier, P. / McDonald, N.Q.
History
DepositionOct 30, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Apr 24, 2019Group: Data collection / Derived calculations / Source and taxonomy
Category: entity_src_gen / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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_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)41,0032
Polymers40,7211
Non-polymers2811
Water905
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)82,0064
Polymers81,4432
Non-polymers5632
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3730 Å2
ΔGint-21.9 kcal/mol
Surface area24510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.569, 98.569, 146.301
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

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


Mass: 40721.398 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 659-1013
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: P07949, receptor protein-tyrosine kinase
#2: Chemical ChemComp-PP1 / 1-TER-BUTYL-3-P-TOLYL-1H-PYRAZOLO[3,4-D]PYRIMIDIN-4-YLAMINE


Mass: 281.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H19N5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.17 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.95→40 Å / Num. obs: 9361 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.9 % / Biso Wilson estimate: 77.33 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.9

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 2.95→34.665 Å / SU ML: 0.35 / σ(F): 1.36 / Phase error: 22.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2244 447 4.8 %
Rwork0.1991 --
obs0.2004 9360 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.95→34.665 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2124 0 21 5 2150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022196
X-RAY DIFFRACTIONf_angle_d0.6652992
X-RAY DIFFRACTIONf_dihedral_angle_d14.5321279
X-RAY DIFFRACTIONf_chiral_restr0.04333
X-RAY DIFFRACTIONf_plane_restr0.003372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.37660.28991340.25042885X-RAY DIFFRACTION100
3.3766-4.25290.25381650.20572905X-RAY DIFFRACTION100
4.2529-34.66740.19251480.18253123X-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)
10.05730.01580.02780.0569-0.15110.2814-0.25470.0371-0.07040.11160.2914-0.83680.12520.42740.00990.39610.04220.01260.3078-0.01080.5892.7351-36.44371.2382
20.3405-0.1047-0.10770.666-0.27290.9298-0.0208-0.0354-0.2174-0.0044-0.1196-0.1354-0.03370.1096-0.12530.2930.00990.13090.2527-0.05530.47140.9601-35.3626-3.7082
30.2812-0.13230.19160.0735-0.16530.5648-0.16230.19810.1799-0.40640.01610.1371-0.13210.53790.08090.6291-0.11990.05620.34270.14850.6966-1.1722-21.731-13.8269
40.3192-0.12680.29370.5603-0.09440.22740.4580.8191-0.1333-0.1304-0.15020.2626-0.18250.03180.07990.59510.06940.11170.5604-0.09470.3892-5.6349-30.6124-20.8376
51.5271-0.74870.16780.6724-0.17070.25230.0836-0.109-0.28390.0173-0.01380.75590.0922-0.20920.10910.57720.0762-0.02030.4079-0.1180.434-19.101-33.3051-14.8279
60.35160.1218-0.10160.29730.02430.1518-0.36970.7884-0.1898-0.20530.22480.2991-0.1589-0.0741-0.18960.86210.3259-0.29460.925-0.10680.1989-23.6139-26.5208-26.5482
70.2882-0.0371-0.12530.245-0.11240.13330.55010.27750.1284-0.22240.0785-0.10330.0488-0.11370.15880.88440.07390.00841.0606-0.23540.5041-7.9419-30.3057-33.8916
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 707 THROUGH 735 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 736 THROUGH 800 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 801 THROUGH 847 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 848 THROUGH 890 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 891 THROUGH 956 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 957 THROUGH 997 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 998 THROUGH 1011 )

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