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- PDB-1nu2: Crystal structure of the murine Disabled-1 (Dab1) PTB domain-ApoE... -

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Basic information

Entry
Database: PDB / ID: 1nu2
TitleCrystal structure of the murine Disabled-1 (Dab1) PTB domain-ApoER2 peptide-PI-4,5P2 ternary complex
Components
  • Disabled homolog 1DAB1
  • peptide derived from murine Apolipoprotein E Receptor-2
KeywordsSIGNALING PROTEIN / beta-sandwich
Function / homology
Function and homology information


cell-cell adhesion involved in neuronal-glial interactions involved in cerebral cortex radial glia guided migration / lateral motor column neuron migration / radial glia guided migration of Purkinje cell / Reelin signalling pathway / cerebral cortex radially oriented cell migration / cerebellum structural organization / Golgi localization / ventral spinal cord development / radial glia-guided pyramidal neuron migration / negative regulation of axonogenesis ...cell-cell adhesion involved in neuronal-glial interactions involved in cerebral cortex radial glia guided migration / lateral motor column neuron migration / radial glia guided migration of Purkinje cell / Reelin signalling pathway / cerebral cortex radially oriented cell migration / cerebellum structural organization / Golgi localization / ventral spinal cord development / radial glia-guided pyramidal neuron migration / negative regulation of axonogenesis / motor neuron migration / negative regulation of receptor signaling pathway via JAK-STAT / negative regulation of cell adhesion / astrocyte differentiation / adult walking behavior / small GTPase-mediated signal transduction / dendrite development / cerebral cortex cell migration / brush border / cell surface receptor signaling pathway via JAK-STAT / negative regulation of astrocyte differentiation / phosphatidylinositol 3-kinase binding / positive regulation of neuron differentiation / SH2 domain binding / axonogenesis / central nervous system development / hippocampus development / phospholipid binding / neuron migration / neuron differentiation / apical part of cell / nervous system development / cell adhesion / intracellular signal transduction / intracellular membrane-bounded organelle / neuronal cell body / perinuclear region of cytoplasm / cytoplasm
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 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like 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 / 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 / Disabled homolog 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsStolt, P.C. / Jeon, H. / Song, H.K. / Herz, J. / Eck, M.J. / Blacklow, S.C.
CitationJournal: Structure / Year: 2003
Title: Origins of Peptide Selectivity and Phosphoinositide Binding Revealed by Structures of Disabled-1 PTB Domain Complexes
Authors: Stolt, P.C. / Jeon, H. / Song, H.K. / Herz, J. / Eck, M.J. / Blacklow, S.C.
History
DepositionJan 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Aug 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
Revision 1.5Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Disabled homolog 1
B: peptide derived from murine Apolipoprotein E Receptor-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7603
Polymers18,3402
Non-polymers4201
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-5 kcal/mol
Surface area8690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.270, 45.984, 89.808
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 Disabled homolog 1 / DAB1


Mass: 17084.768 Da / Num. of mol.: 1 / Fragment: residues 23-174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: DAB1 / Plasmid: Gateway pDEST15 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P97318
#2: Protein/peptide peptide derived from murine Apolipoprotein E Receptor-2


Mass: 1255.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: created by peptide synthesis
#3: Chemical ChemComp-I3P / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Inositol trisphosphate


Mass: 420.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15O15P3 / Details: purchased from Sigma-Aldrich Chemical Co.
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 1.8 Å3/Da / Density % sol: 31.08 %
Crystal growTemperature: 298 K / pH: 7.5
Details: HEPES, PEG8000, ethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.50
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115-25 mg/mlprotein1drop
250 mMTris1droppH6.8
350 mM1dropNaCl
45 mMdithiothreitol1drop
50.1 MHEPES1droppH7.5
634-36 %PEG80001drop
75 %ethanol1drop
80.1 MHEPES1reservoirpH7.5
934-36 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 29, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 12179 / % possible obs: 98 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.047
Reflection shellResolution: 1.9→1.96 Å / Rmerge(I) obs: 0.17 / % possible all: 97.5
Reflection
*PLUS
Lowest resolution: 40 Å / % possible obs: 98 % / Num. measured all: 34852
Reflection shell
*PLUS
% possible obs: 97.5 % / Rmerge(I) obs: 0.17

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NTV

1ntv


Resolution: 1.9→40 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1228 10.3 %RANDOM
Rwork0.204 ---
all0.2384 ---
obs0.2384 11884 95.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.9985 Å2 / ksol: 0.383678 e/Å3
Displacement parametersBiso mean: 25.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å20 Å20 Å2
2--6.21 Å20 Å2
3----4.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-40 Å
Luzzati sigma a0.14 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1288 0 48 141 1477
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.66
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.9→1.96 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.27 85 9.5 %
Rwork0.227 807 -
obs--90.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3I3P.PARWATER.TOP
X-RAY DIFFRACTION4WATER.PARAMI3P.TOP
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 40 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.08
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.66

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