[English] 日本語
Yorodumi
- PDB-1oqn: Crystal structure of the phosphotyrosine binding domain (PTB) of ... -

+
Open data


ID or keywords:

Loading...

-
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 / lateral motor column neuron migration / Reelin signalling pathway / radial glia guided migration of Purkinje cell / 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 ...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 / lateral motor column neuron migration / Reelin signalling pathway / radial glia guided migration of Purkinje cell / 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 / negative regulation of presynapse assembly / Mitochondrial protein degradation / Platelet degranulation / cytosolic mRNA polyadenylation / Golgi localization / cerebellum structural organization / synaptic assembly at neuromuscular junction / radial glia-guided pyramidal neuron migration / Lysosome Vesicle Biogenesis / smooth endoplasmic reticulum calcium ion homeostasis / cerebral cortex radially oriented cell migration / ventral spinal cord development / negative regulation of axonogenesis / lipoprotein particle / regulation of amyloid-beta clearance / motor neuron migration / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / ciliary rootlet / reelin-mediated signaling pathway / negative regulation of receptor signaling pathway via JAK-STAT / regulation of synapse maturation / negative regulation of cell adhesion / COPII-coated ER to Golgi transport vesicle / astrocyte differentiation / suckling behavior / frizzled binding / amyloid-beta complex / growth cone lamellipodium / heparan sulfate proteoglycan binding / cellular response to norepinephrine stimulus / growth cone filopodium / microglia development / collateral sprouting in absence of injury / axo-dendritic transport / regulation of synapse structure or activity / axon midline choice point recognition / astrocyte activation involved in immune response / G alpha (q) signalling events / central nervous system neuron differentiation / presynaptic active zone / regulation of spontaneous synaptic transmission / mating behavior / G alpha (i) signalling events / adult walking behavior / growth factor receptor binding / peptidase activator activity / Golgi-associated vesicle / PTB domain binding / neuromuscular process controlling balance / positive regulation of amyloid fibril formation / astrocyte projection / small GTPase-mediated signal transduction / neuron remodeling / negative regulation of neuron differentiation / negative regulation of astrocyte differentiation / nuclear envelope lumen / spindle midzone / intracellular vesicle / forebrain development / dendrite development / positive regulation of protein metabolic process / cerebral cortex cell migration / smooth endoplasmic reticulum / signaling receptor activator activity / negative regulation of long-term synaptic potentiation / modulation of excitatory postsynaptic potential / apolipoprotein binding / main axon / transition metal ion binding / intracellular copper ion homeostasis / regulation of multicellular organism growth / positive regulation of G2/M transition of mitotic cell cycle / cell surface receptor signaling pathway via JAK-STAT / regulation of presynapse assembly / positive regulation of T cell migration / neuronal dense core vesicle / cholesterol metabolic process / positive regulation of chemokine production / cellular response to manganese ion / Notch signaling pathway / clathrin-coated pit / signaling adaptor activity / extracellular matrix organization / neuron projection maintenance / positive regulation of neuron differentiation / astrocyte activation / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more