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Yorodumi- PDB-4mdr: Crystal structure of adaptor protein complex 4 (AP-4) mu4 subunit... -
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-Basic information
Entry | Database: PDB / ID: 4mdr | ||||||
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Title | Crystal structure of adaptor protein complex 4 (AP-4) mu4 subunit C-terminal domain D190A mutant, in complex with a sorting peptide from the amyloid precursor protein (APP) | ||||||
Components |
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Keywords | PROTEIN TRANSPORT/PROTEIN BINDING / immunoglobulin-like beta-sandwich / adaptor protein complex / Golgi apparatus / sorting signal recognition / Alzheimer's disease / amyloid precursor protein / PROTEIN TRANSPORT-PROTEIN BINDING complex | ||||||
Function / homology | Function and homology information AP-4 adaptor complex / protein localization to basolateral plasma membrane / Golgi to lysosome transport / clathrin adaptor complex / post-Golgi vesicle-mediated transport / Golgi to endosome transport / protein targeting to lysosome / regulation of epidermal growth factor-activated receptor activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury ...AP-4 adaptor complex / protein localization to basolateral plasma membrane / Golgi to lysosome transport / clathrin adaptor complex / post-Golgi vesicle-mediated transport / Golgi to endosome transport / protein targeting to lysosome / regulation of epidermal growth factor-activated receptor activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / signaling receptor activator activity / axon midline choice point recognition / smooth endoplasmic reticulum calcium ion homeostasis / astrocyte activation involved in immune response / regulation of spontaneous synaptic transmission / mating behavior / NMDA selective glutamate receptor signaling pathway / ciliary rootlet / Lysosome Vesicle Biogenesis / PTB domain binding / Golgi-associated vesicle / neuron remodeling / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of amyloid fibril formation / positive regulation of G2/M transition of mitotic cell cycle / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / COPII-coated ER to Golgi transport vesicle / suckling behavior / dendrite development / presynaptic active zone / modulation of excitatory postsynaptic potential / regulation of peptidyl-tyrosine phosphorylation / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / neuromuscular process controlling balance / The NLRP3 inflammasome / regulation of presynapse assembly / transition metal ion binding / protein transmembrane transporter activity / negative regulation of long-term synaptic potentiation / regulation of multicellular organism growth / autophagosome assembly / negative regulation of neuron differentiation / ECM proteoglycans / intracellular copper ion homeostasis / smooth endoplasmic reticulum / positive regulation of T cell migration / spindle midzone / protein targeting / Purinergic signaling in leishmaniasis infection / protein serine/threonine kinase binding / positive regulation of chemokine production / clathrin-coated pit / forebrain development / vesicle-mediated transport / Notch signaling pathway / neuron projection maintenance / positive regulation of protein metabolic process / positive regulation of calcium-mediated signaling / astrocyte activation / ionotropic glutamate receptor signaling pathway / positive regulation of glycolytic process / response to interleukin-1 / cholesterol metabolic process / positive regulation of mitotic cell cycle / extracellular matrix organization / adult locomotory behavior / axonogenesis / platelet alpha granule lumen / trans-Golgi network membrane / positive regulation of peptidyl-threonine phosphorylation / positive regulation of interleukin-1 beta production / learning / dendritic shaft / positive regulation of long-term synaptic potentiation / Mitochondrial protein degradation / central nervous system development / locomotory behavior / endosome lumen / positive regulation of JNK cascade / Post-translational protein phosphorylation / intracellular protein transport / synapse organization / microglial cell activation / regulation of long-term neuronal synaptic plasticity / TAK1-dependent IKK and NF-kappa-B activation / visual learning / trans-Golgi network / neuromuscular junction / positive regulation of non-canonical NF-kappaB signal transduction / recycling endosome / cognition / G2/M transition of mitotic cell cycle Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Ross, B.H. / Lin, Y. / Corales, E.A. / Burgos, P.V. / Mardones, G.A. | ||||||
Citation | Journal: Plos One / Year: 2014 Title: Structural and Functional Characterization of Cargo-Binding Sites on the mu 4-Subunit of Adaptor Protein Complex 4. Authors: Ross, B.H. / Lin, Y. / Corales, E.A. / Burgos, P.V. / Mardones, G.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mdr.cif.gz | 67.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mdr.ent.gz | 48.2 KB | Display | PDB format |
PDBx/mmJSON format | 4mdr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mdr_validation.pdf.gz | 435.3 KB | Display | wwPDB validaton report |
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Full document | 4mdr_full_validation.pdf.gz | 438.3 KB | Display | |
Data in XML | 4mdr_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 4mdr_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/md/4mdr ftp://data.pdbj.org/pub/pdb/validation_reports/md/4mdr | HTTPS FTP |
-Related structure data
Related structure data | 3l81S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33068.637 Da / Num. of mol.: 1 / Fragment: C-terminus, residues 160-453 / Mutation: D190A,C235S,C431S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AP4M1, MUARP2 / Production host: Escherichia coli (E. coli) / References: UniProt: O00189 |
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#2: Protein/peptide | Mass: 1303.394 Da / Num. of mol.: 1 / Fragment: C-terminus, residues 761-767 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: P05067 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.41 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 15% PEG 6000, 3% trimethylamine N-oxide dihydrate, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 1, 2009 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→50 Å / Num. all: 25791 / Num. obs: 25043 / % possible obs: 97.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.077 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.84→1.91 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.7 / % possible all: 75.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3L81 Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.586 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.49 Å2 / Biso mean: 36.567 Å2 / Biso min: 17.72 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.853→1.901 Å / Total num. of bins used: 20
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