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- PDB-1oqn: Crystal structure of the phosphotyrosine binding domain (PTB) of ... -

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Basic information

Entry
Database: PDB / ID: 1oqn
TitleCrystal structure of the phosphotyrosine binding domain (PTB) of mouse Disabled 1 (Dab1)
Components
  • Alzheimer's disease amyloid A4 protein homolog
  • Disabled homolog 1
KeywordsSIGNALING PROTEIN / PTB / Inositol / APP
Function / homology
Function and homology information


cell-cell adhesion involved in neuronal-glial interactions involved in cerebral cortex radial glia guided migration / Formyl peptide receptors bind formyl peptides and many other ligands / growth cone lamellipodium / cellular response to norepinephrine stimulus / lateral motor column neuron migration / Reelin signalling pathway / ECM proteoglycans / radial glia guided migration of Purkinje cell / growth cone filopodium / TAK1-dependent IKK and NF-kappa-B activation ...cell-cell adhesion involved in neuronal-glial interactions involved in cerebral cortex radial glia guided migration / Formyl peptide receptors bind formyl peptides and many other ligands / growth cone lamellipodium / cellular response to norepinephrine stimulus / lateral motor column neuron migration / Reelin signalling pathway / ECM proteoglycans / radial glia guided migration of Purkinje cell / growth cone filopodium / TAK1-dependent IKK and NF-kappa-B activation / Post-translational protein phosphorylation / TRAF6 mediated NF-kB activation / endosome to plasma membrane transport vesicle / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Advanced glycosylation endproduct receptor signaling / Mitochondrial protein degradation / Platelet degranulation / Golgi localization / cerebellum structural organization / radial glia-guided pyramidal neuron migration / Lysosome Vesicle Biogenesis / ventral spinal cord development / cerebral cortex radially oriented cell migration / negative regulation of axonogenesis / lipoprotein particle / regulation of amyloid-beta clearance / motor neuron migration / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / growth factor receptor binding / peptidase activator activity / reelin-mediated signaling pathway / negative regulation of receptor signaling pathway via JAK-STAT / astrocyte projection / negative regulation of cell adhesion / central nervous system neuron differentiation / regulation of synapse maturation / astrocyte differentiation / frizzled binding / heparan sulfate proteoglycan binding / amyloid-beta complex / microglia development / negative regulation of presynapse assembly / collateral sprouting in absence of injury / cytosolic mRNA polyadenylation / synaptic assembly at neuromuscular junction / regulation of synapse structure or activity / axo-dendritic transport / axon midline choice point recognition / G alpha (q) signalling events / astrocyte activation involved in immune response / smooth endoplasmic reticulum calcium ion homeostasis / regulation of spontaneous synaptic transmission / G alpha (i) signalling events / mating behavior / adult walking behavior / main axon / ciliary rootlet / Golgi-associated vesicle / PTB domain binding / positive regulation of amyloid fibril formation / small GTPase-mediated signal transduction / neuron remodeling / nuclear envelope lumen / suckling behavior / negative regulation of astrocyte differentiation / COPII-coated ER to Golgi transport vesicle / intracellular vesicle / neuronal dense core vesicle / positive regulation of protein metabolic process / dendrite development / cerebral cortex cell migration / modulation of excitatory postsynaptic potential / presynaptic active zone / signaling receptor activator activity / negative regulation of long-term synaptic potentiation / apolipoprotein binding / neuromuscular process controlling balance / transition metal ion binding / regulation of multicellular organism growth / intracellular copper ion homeostasis / regulation of presynapse assembly / cellular response to manganese ion / negative regulation of neuron differentiation / cell surface receptor signaling pathway via JAK-STAT / spindle midzone / positive regulation of T cell migration / forebrain development / smooth endoplasmic reticulum / positive regulation of chemokine production / cellular response to copper ion / cellular response to cAMP / clathrin-coated pit / Notch signaling pathway / positive regulation of G2/M transition of mitotic cell cycle / signaling adaptor activity / extracellular matrix organization / neuron projection maintenance / positive regulation of neuron differentiation / ionotropic glutamate receptor signaling pathway / SH2 domain binding
Similarity search - Function
: / : / Disabled homolog 2-like, sulfatide-binding motifs / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily ...: / : / Disabled homolog 2-like, sulfatide-binding motifs / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site / Beta-amyloid precursor protein C-terminus / Amyloid precursor protein (APP) intracellular domain signature. / Amyloidogenic glycoprotein, extracellular / Amyloidogenic glycoprotein, heparin-binding / Amyloidogenic glycoprotein, E2 domain / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / Amyloid A4 N-terminal heparin-binding / E2 domain of amyloid precursor protein / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / amyloid A4 / Amyloidogenic glycoprotein / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Amyloid-beta precursor protein / Disabled homolog 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYun, M. / Keshvara, L. / Park, C.-G. / Zhang, Y.-M. / Dickerson, J.B. / Zheng, J. / Rock, C.O. / Curran, T. / Park, H.-W.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal structures of the Dab homology domains of mouse disabled 1 and 2
Authors: Yun, M. / Keshvara, L. / Park, C.-G. / Zhang, Y.-M. / Dickerson, J.B. / Zheng, J. / Rock, C.O. / Curran, T. / Park, H.-W.
History
DepositionMar 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Disabled homolog 1
B: Disabled homolog 1
C: Alzheimer's disease amyloid A4 protein homolog
D: Alzheimer's disease amyloid A4 protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9346
Polymers38,0944
Non-polymers8402
Water3,909217
1
A: Disabled homolog 1
C: Alzheimer's disease amyloid A4 protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4673
Polymers19,0472
Non-polymers4201
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-1 kcal/mol
Surface area9370 Å2
MethodPISA
2
B: Disabled homolog 1
D: Alzheimer's disease amyloid A4 protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4673
Polymers19,0472
Non-polymers4201
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-2 kcal/mol
Surface area9370 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-8 kcal/mol
Surface area17570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.106, 66.481, 90.528
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Disabled homolog 1 / Dab1


Mass: 17960.758 Da / Num. of mol.: 2 / Fragment: PTB domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P97318
#2: Protein/peptide Alzheimer's disease amyloid A4 protein homolog / APP / Amyloidogenic glycoprotein / AG


Mass: 1086.132 Da / Num. of mol.: 2 / Fragment: 9mer peptide / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Rattus norvegicus (rat).
References: UniProt: P08592
#3: Chemical ChemComp-I3P / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE


Mass: 420.096 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15O15P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 3350, magnesium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mMHEPES1droppH7.5
21 mMdithiothreitol1drop
31 mMEDTA1drop
420 mg/mlprotein1drop
520 %(w/v)PEG33501reservoir
60.2 Mtri-lithium citrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.00465 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 20, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00465 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 16118 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 24.8 % / Rsym value: 0.077 / Net I/σ(I): 27.3
Reflection
*PLUS
Num. measured all: 400319 / Rmerge(I) obs: 0.077

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
EPMRphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M7E

1m7e


Resolution: 2.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflectionSelection details
Rfree0.303 618 RANDOM
Rwork0.246 --
all-16118 -
obs-13125 -
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2538 0 48 217 2803
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.263
X-RAY DIFFRACTIONc_dihedral_angle_d23.844
X-RAY DIFFRACTIONc_improper_angle_d0.699
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.26
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.844
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.699

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