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- PDB-1m7e: Crystal structure of the phosphotyrosine binding domain(PTB) of m... -

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Basic information

Entry
Database: PDB / ID: 1m7e
TitleCrystal structure of the phosphotyrosine binding domain(PTB) of mouse Disabled 2(Dab2):implications for Reeling signaling
Components
  • Disabled homolog 2
  • NGYENPTYK peptide
KeywordsSIGNALING PROTEIN / PTB / Protein-peptide complex
Function / homology
Function and homology information


positive regulation of protein import / Formyl peptide receptors bind formyl peptides and many other ligands / regulation of neurotransmitter uptake / regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of response to endoplasmic reticulum stress / positive regulation of aldosterone biosynthetic process / positive regulation of gene expression, epigenetic / positive regulation of aldosterone secretion / leading edge cell differentiation / ECM proteoglycans ...positive regulation of protein import / Formyl peptide receptors bind formyl peptides and many other ligands / regulation of neurotransmitter uptake / regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of response to endoplasmic reticulum stress / positive regulation of aldosterone biosynthetic process / positive regulation of gene expression, epigenetic / positive regulation of aldosterone secretion / leading edge cell differentiation / ECM proteoglycans / 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 / low-density lipoprotein particle mediated signaling / negative regulation of presynapse assembly / Mitochondrial protein degradation / Platelet degranulation / Formation of annular gap junctions / cytosolic mRNA polyadenylation / Gap junction degradation / pinocytosis / regulation of dendritic spine maintenance / negative regulation of blood circulation / positive regulation of endothelin production / positive regulation of clathrin-dependent endocytosis / positive regulation of Toll signaling pathway / synaptic assembly at neuromuscular junction / phospholipase D-activating G protein-coupled receptor signaling pathway / positive regulation of G protein-coupled receptor internalization / positive regulation of early endosome to late endosome transport / protein trimerization / renal protein absorption / Lysosome Vesicle Biogenesis / smooth endoplasmic reticulum calcium ion homeostasis / positive regulation of integrin-mediated signaling pathway / AP-2 adaptor complex binding / positive regulation of amyloid precursor protein catabolic process / clathrin coat of coated pit / lipoprotein particle / regulation of amyloid-beta clearance / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / intermediate-density lipoprotein particle / Cargo recognition for clathrin-mediated endocytosis / positive regulation of Wnt signaling pathway, planar cell polarity pathway / Clathrin-mediated endocytosis / clathrin-coated vesicle membrane / clathrin coat assembly / RAGE receptor binding / clathrin-cargo adaptor activity / ciliary rootlet / negative regulation of androgen receptor signaling pathway / regulation of amyloid fibril formation / positive regulation of G protein-coupled receptor signaling pathway / endoderm development / myeloid cell differentiation / low-density lipoprotein particle / high-density lipoprotein particle / COPII-coated ER to Golgi transport vesicle / very-low-density lipoprotein particle / acetylcholine receptor binding / frizzled binding / heparan sulfate proteoglycan binding / amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / suckling behavior / growth cone filopodium / positive regulation of monocyte chemotaxis / microglia development / collateral sprouting in absence of injury / axo-dendritic transport / hippocampal neuron apoptotic process / response to steroid hormone / positive regulation of membrane protein ectodomain proteolysis / axon midline choice point recognition / astrocyte activation involved in immune response / regulation of synapse structure or activity / negative regulation of protein localization to nucleus / G alpha (q) signalling events / central nervous system neuron differentiation / clathrin-coated vesicle / presynaptic active zone / regulation of spontaneous synaptic transmission / mating behavior / G alpha (i) signalling events / cargo receptor activity / positive regulation of extrinsic apoptotic signaling pathway / growth factor receptor binding / peptidase activator activity / Golgi-associated vesicle / neuromuscular process controlling balance / PTB domain binding / low-density lipoprotein particle receptor binding / positive regulation of amyloid fibril formation / clathrin binding / astrocyte projection / regulation of toll-like receptor signaling pathway
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
Amyloid-beta precursor protein / Disabled homolog 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SIR / Resolution: 2.45 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
DepositionJul 19, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Disabled homolog 2
B: Disabled homolog 2
C: Disabled homolog 2
D: NGYENPTYK peptide
E: NGYENPTYK peptide
F: NGYENPTYK peptide


Theoretical massNumber of molelcules
Total (without water)57,3866
Polymers57,3866
Non-polymers00
Water3,603200
1
A: Disabled homolog 2
D: NGYENPTYK peptide


Theoretical massNumber of molelcules
Total (without water)19,1292
Polymers19,1292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-6 kcal/mol
Surface area8890 Å2
MethodPISA
2
B: Disabled homolog 2
E: NGYENPTYK peptide


Theoretical massNumber of molelcules
Total (without water)19,1292
Polymers19,1292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-5 kcal/mol
Surface area8840 Å2
MethodPISA
3
C: Disabled homolog 2
F: NGYENPTYK peptide


Theoretical massNumber of molelcules
Total (without water)19,1292
Polymers19,1292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-6 kcal/mol
Surface area8770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.258, 127.258, 269.541
Angle α, β, γ (deg.)90, 90, 120
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Disabled homolog 2 / DOC-2 / Mitogen-responsive phosphoprotein / DAB2


Mass: 18042.629 Da / Num. of mol.: 3
Fragment: Phosphotyrosine binding domain (PTB), Residues 33-191
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: P98078
#2: Protein/peptide NGYENPTYK peptide


Mass: 1086.132 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / References: UniProt: P08592*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 3.66 Å3/Da / Density % sol: 66.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: sodium formate, pH 8.5, 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
53.8 Msodium formate1reservoir
650 mMHEPES1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å
DetectorType: MAC Science DIP-2000 / Detector: IMAGE PLATE / Date: Sep 30, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→20 Å / Num. all: 31089 / Num. obs: 31089 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 22.9 % / Rsym value: 0.1 / Net I/σ(I): 21.6
Reflection shellResolution: 2.45→2.5 Å / % possible all: 88.2
Reflection
*PLUS
Num. measured all: 712193 / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 88.2 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: SIR / Resolution: 2.45→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.273 -RANDOM
Rwork0.244 --
obs-28091 -
Refinement stepCycle: LAST / Resolution: 2.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3789 0 0 200 3989
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0074
X-RAY DIFFRACTIONc_angle_deg1.2129
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.272
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.21

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