+Open data
-Basic information
Entry | Database: PDB / ID: 1x11 | ||||||
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Title | X11 PTB DOMAIN | ||||||
Components |
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Keywords | COMPLEX (PEPTIDE BINDING MODULE/PEPTIDE) / COMPLEX (PEPTIDE BINDING MODULE-PEPTIDE) / PTB DOMAIN / COMPLEX (PEPTIDE BINDING MODULE-PEPTIDE) complex | ||||||
Function / homology | Function and homology information gamma-aminobutyric acid secretion / Dopamine Neurotransmitter Release Cycle / NMDA selective glutamate receptor signaling pathway / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway / axo-dendritic transport / glutamate secretion ...gamma-aminobutyric acid secretion / Dopamine Neurotransmitter Release Cycle / NMDA selective glutamate receptor signaling pathway / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway / axo-dendritic transport / glutamate secretion / synaptic assembly at neuromuscular junction / Formyl peptide receptors bind formyl peptides and many other ligands / signaling receptor activator activity / Assembly and cell surface presentation of NMDA receptors / axon midline choice point recognition / smooth endoplasmic reticulum calcium ion homeostasis / Neurexins and neuroligins / astrocyte activation involved in immune response / regulation of spontaneous synaptic transmission / mating behavior / Lysosome Vesicle Biogenesis / ciliary rootlet / PTB domain binding / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / Golgi-associated vesicle / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of amyloid fibril formation / neuron remodeling / COPII-coated ER to Golgi transport vesicle / suckling behavior / nuclear envelope lumen / dendrite development / presynaptic active zone / modulation of excitatory postsynaptic potential / TRAF6 mediated NF-kB activation / The NLRP3 inflammasome / neuromuscular process controlling balance / Advanced glycosylation endproduct receptor signaling / transition metal ion binding / regulation of presynapse assembly / negative regulation of long-term synaptic potentiation / negative regulation of neuron differentiation / regulation of multicellular organism growth / intracellular copper ion homeostasis / ECM proteoglycans / trans-Golgi network membrane / smooth endoplasmic reticulum / positive regulation of T cell migration / spindle midzone / Purinergic signaling in leishmaniasis infection / clathrin-coated pit / protein serine/threonine kinase binding / regulation of peptidyl-tyrosine phosphorylation / positive regulation of chemokine production / presynaptic active zone membrane / forebrain development / Notch signaling pathway / neuron projection maintenance / Mitochondrial protein degradation / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of protein metabolic process / presynaptic modulation of chemical synaptic transmission / cholesterol metabolic process / positive regulation of calcium-mediated signaling / ionotropic glutamate receptor signaling pathway / response to interleukin-1 / positive regulation of glycolytic process / axonogenesis / positive regulation of mitotic cell cycle / extracellular matrix organization / adult locomotory behavior / platelet alpha granule lumen / positive regulation of interleukin-1 beta production / learning / positive regulation of peptidyl-threonine phosphorylation / dendritic shaft / positive regulation of long-term synaptic potentiation / cognition / central nervous system development / endosome lumen / locomotory behavior / intracellular protein transport / astrocyte activation / Post-translational protein phosphorylation / positive regulation of JNK cascade / microglial cell activation / regulation of long-term neuronal synaptic plasticity / synapse organization / serine-type endopeptidase inhibitor activity / TAK1-dependent IKK and NF-kappa-B activation / visual learning / neuromuscular junction / multicellular organism growth / Schaffer collateral - CA1 synapse / recycling endosome / positive regulation of interleukin-6 production / Golgi lumen / positive regulation of inflammatory response / neuron cellular homeostasis / positive regulation of non-canonical NF-kappaB signal transduction Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MAD / Resolution: 2.5 Å | ||||||
Authors | Lee, C.-H. / Zhang, Z. / Kuriyan, J. | ||||||
Citation | Journal: EMBO J. / Year: 1997 Title: Sequence-specific recognition of the internalization motif of the Alzheimer's amyloid precursor protein by the X11 PTB domain. Authors: Zhang, Z. / Lee, C.H. / Mandiyan, V. / Borg, J.P. / Margolis, B. / Schlessinger, J. / Kuriyan, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1x11.cif.gz | 89.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1x11.ent.gz | 69 KB | Display | PDB format |
PDBx/mmJSON format | 1x11.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1x11_validation.pdf.gz | 423.2 KB | Display | wwPDB validaton report |
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Full document | 1x11_full_validation.pdf.gz | 432 KB | Display | |
Data in XML | 1x11_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 1x11_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x1/1x11 ftp://data.pdbj.org/pub/pdb/validation_reports/x1/1x11 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.28, -0.569, 0.773), Vector: |
-Components
#1: Protein | Mass: 19801.256 Da / Num. of mol.: 2 / Fragment: PTB DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q02410 #2: Protein/peptide | Mass: 1637.723 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source References: UniProt: P05067 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.19 % | ||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Aug 1, 1996 / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 97157 / % possible obs: 99.3 % / Redundancy: 5.5 % / Rsym value: 0.054 / Net I/σ(I): 27.6 |
Reflection shell | Resolution: 2.4→2.49 Å / Mean I/σ(I) obs: 5.1 / Rsym value: 0.302 / % possible all: 99.2 |
Reflection | *PLUS Num. obs: 17790 / Num. measured all: 97157 / Rmerge(I) obs: 0.054 |
Reflection shell | *PLUS % possible obs: 99.2 % / Rmerge(I) obs: 0.302 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.5→6 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 Details: MISSING RESIDUES CORRESPOND TO DISORDERED REGIONS THAT WERE NOT MODELLED.
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Displacement parameters | Biso mean: 42.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→6 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.232 / Rfactor obs: 0.212 / Rfactor Rfree: 0.303 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS % reflection Rfree: 10 % |