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- PDB-1uef: Crystal Structure of Dok1 PTB Domain Complex -

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Basic information

Entry
Database: PDB / ID: 1uef
TitleCrystal Structure of Dok1 PTB Domain Complex
Components
  • 13-mer peptide from Proto-oncogene tyrosine-protein kinase receptor ret
  • Docking protein 1
KeywordsPROTEIN BINDING/TRANSFERASE / protein binding / transferase / phosphotyrosine binding domain / PROTEIN BINDING-TRANSFERASE COMPLEX
Function / homology
Function and homology information


PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / : / macrophage colony-stimulating factor signaling pathway / Peyer's patch morphogenesis / positive regulation of metanephric glomerulus development / ureter maturation / embryonic epithelial tube formation / glial cell-derived neurotrophic factor receptor signaling pathway / membrane protein proteolysis / positive regulation of peptidyl-serine phosphorylation of STAT protein ...PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / : / macrophage colony-stimulating factor signaling pathway / Peyer's patch morphogenesis / positive regulation of metanephric glomerulus development / ureter maturation / embryonic epithelial tube formation / glial cell-derived neurotrophic factor receptor signaling pathway / membrane protein proteolysis / positive regulation of peptidyl-serine phosphorylation of STAT protein / RAF/MAP kinase cascade / positive regulation of neuron maturation / response to xenobiotic stimulus => GO:0009410 / enteric nervous system development / neuron cell-cell adhesion / multicellular organism development / RET signaling / innervation / plasma membrane protein complex / neuron maturation / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of kinase activity / positive regulation of cell adhesion mediated by integrin / neural crest cell migration / ureteric bud development / negative regulation of MAPK cascade / response to pain / regulation of axonogenesis / homophilic cell adhesion via plasma membrane adhesion molecules / plasma membrane => GO:0005886 / positive regulation of cell size / anatomical structure morphogenesis / regulation of cell adhesion / cellular response to retinoic acid / transmembrane receptor protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / neuron differentiation / 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 / nervous system development / Ras protein signal transduction / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / early endosome / receptor complex / endosome membrane / intracellular signal transduction / positive regulation of cell migration / membrane raft / axon / neuronal cell body / dendrite / calcium ion binding / positive regulation of gene expression / positive regulation of DNA-templated transcription / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Dok1/2/3, PTB domain / Phosphotyrosine-binding domain (IRS1-like) / IRS-type PTB domain profile. / IRS-type PTB domain / PTB domain (IRS-1 type) / 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 ...Dok1/2/3, PTB domain / Phosphotyrosine-binding domain (IRS1-like) / IRS-type PTB domain profile. / IRS-type PTB domain / PTB domain (IRS-1 type) / 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 / Phosphotyrosine-binding domain / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / Pleckstrin homology domain. / Pleckstrin homology domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / PH-like domain superfamily / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Proto-oncogene tyrosine-protein kinase receptor Ret / Docking protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsShi, N. / Ye, S. / Liu, Y. / Zhou, W. / Ding, Y. / Lou, Z. / Qiang, B. / Yan, J. / Rao, Z.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural Basis for the Specific Recognition of RET by the Dok1 Phosphotyrosine Binding Domain
Authors: Shi, N. / Ye, S. / Bartlam, M. / Yang, M. / Wu, J. / Liu, Y. / Sun, F. / Han, X. / Peng, X. / Qiang, B. / Yuan, J. / Rao, Z.
History
DepositionMay 14, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Docking protein 1
B: Docking protein 1
C: 13-mer peptide from Proto-oncogene tyrosine-protein kinase receptor ret
D: 13-mer peptide from Proto-oncogene tyrosine-protein kinase receptor ret


Theoretical massNumber of molelcules
Total (without water)31,9964
Polymers31,9964
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Docking protein 1
C: 13-mer peptide from Proto-oncogene tyrosine-protein kinase receptor ret


Theoretical massNumber of molelcules
Total (without water)15,9982
Polymers15,9982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-12 kcal/mol
Surface area6350 Å2
MethodPISA
3
B: Docking protein 1
D: 13-mer peptide from Proto-oncogene tyrosine-protein kinase receptor ret


Theoretical massNumber of molelcules
Total (without water)15,9982
Polymers15,9982
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-12 kcal/mol
Surface area6300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.482, 55.720, 99.126
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Docking protein 1


Mass: 14373.210 Da / Num. of mol.: 2 / Fragment: Dok1 PTB Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P97465
#2: Protein/peptide 13-mer peptide from Proto-oncogene tyrosine-protein kinase receptor ret / Polypeptide containing a phosphorylated tyrosine


Mass: 1624.685 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This polypeptide substrate, is synthesized artificially.
References: UniProt: P35546, EC: 2.7.1.112
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.44 Å3/Da / Density % sol: 49.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG6000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 26, 2003
RadiationMonochromator: Melting Silicom +Fuzed Quartz / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 44613 / Num. obs: 43666 / % possible obs: 91 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 %
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.2 % / Num. unique all: 764 / % possible all: 85.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 850 -RANDOM
Rwork0.213 ---
all0.22 44613 --
obs0.22 43666 86.6 %-
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1819 0 0 17 1836
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.1583
X-RAY DIFFRACTIONc_angle_deg2.0716
X-RAY DIFFRACTIONc_dihedral_angle_d25.3743
X-RAY DIFFRACTIONc_improper_angle_d1.2273

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