+Open data
-Basic information
Entry | Database: PDB / ID: 2ipu | ||||||
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Title | PFA1 Fab fragment complexed with Abeta 1-8 peptide | ||||||
Components |
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Keywords | IMMUNE SYSTEM / wwddd / cdr / abeta | ||||||
Function / homology | Function and homology information regulation of epidermal growth factor-activated receptor activity / signaling receptor activator activity / collateral sprouting in absence of injury / cytosolic mRNA polyadenylation / microglia development / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands / regulation of Wnt signaling pathway / axo-dendritic transport / synaptic assembly at neuromuscular junction ...regulation of epidermal growth factor-activated receptor activity / signaling receptor activator activity / collateral sprouting in absence of injury / cytosolic mRNA polyadenylation / microglia development / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands / regulation of Wnt signaling pathway / axo-dendritic transport / synaptic assembly at neuromuscular junction / smooth endoplasmic reticulum calcium ion homeostasis / axon midline choice point recognition / 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 / positive regulation of amyloid fibril formation / neuron remodeling / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / protein serine/threonine kinase binding / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / : / nuclear envelope lumen / suckling behavior / presynaptic active zone / dendrite development / COPII-coated ER to Golgi transport vesicle / modulation of excitatory postsynaptic potential / 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 / regulation of multicellular organism growth / intracellular copper ion homeostasis / negative regulation of long-term synaptic potentiation / negative regulation of neuron differentiation / ECM proteoglycans / smooth endoplasmic reticulum / Mitochondrial protein degradation / positive regulation of T cell migration / spindle midzone / Purinergic signaling in leishmaniasis infection / positive regulation of calcium-mediated signaling / forebrain development / clathrin-coated pit / regulation of peptidyl-tyrosine phosphorylation / positive regulation of chemokine production / Notch signaling pathway / positive regulation of G2/M transition of mitotic cell cycle / neuron projection maintenance / positive regulation of protein metabolic process / ionotropic glutamate receptor signaling pathway / positive regulation of glycolytic process / cholesterol metabolic process / response to interleukin-1 / positive regulation of mitotic cell cycle / extracellular matrix organization / axonogenesis / adult locomotory behavior / trans-Golgi network membrane / dendritic shaft / platelet alpha granule lumen / locomotory behavior / positive regulation of peptidyl-threonine phosphorylation / learning / positive regulation of interleukin-1 beta production / central nervous system development / positive regulation of long-term synaptic potentiation / endosome lumen / astrocyte activation / Post-translational protein phosphorylation / positive regulation of JNK cascade / synapse organization / regulation of long-term neuronal synaptic plasticity / microglial cell activation / TAK1-dependent IKK and NF-kappa-B activation / visual learning / serine-type endopeptidase inhibitor activity / neuromuscular junction / recycling endosome / cognition / positive regulation of inflammatory response / Golgi lumen / neuron cellular homeostasis / endocytosis / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to amyloid-beta / positive regulation of interleukin-6 production / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / neuron projection development / G2/M transition of mitotic cell cycle / positive regulation of tumor necrosis factor production / cell-cell junction / synaptic vesicle Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Gardberg, A.S. / Dealwis, C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007 Title: Molecular basis for passive immunotherapy of Alzheimer's disease Authors: Gardberg, A.S. / Dice, L.T. / Ou, S. / Rich, R.L. / Helmbrecht, E. / Ko, J. / Wetzel, R. / Myszka, D.G. / Patterson, P.H. / Dealwis, C. | ||||||
History |
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Remark 999 | SEQUENCE Presently, there is no aminoacid sequence database reference available for the two ...SEQUENCE Presently, there is no aminoacid sequence database reference available for the two proteins IGG2A FAB fragment heavy chain and IGG2A FAB fragment light chain kappa |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ipu.cif.gz | 181.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ipu.ent.gz | 144.5 KB | Display | PDB format |
PDBx/mmJSON format | 2ipu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/2ipu ftp://data.pdbj.org/pub/pdb/validation_reports/ip/2ipu | HTTPS FTP |
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-Related structure data
Related structure data | 2iptC 2iq9SC 2iqaC 2r0wC 2r0zC 2iqb C: citing same article (ref.) 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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2 |
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Unit cell |
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Details | The biological assembly is a heterodimer with abeta peptide at the interface. |
-Components
-Protein/peptide , 1 types, 2 molecules PQ
#3: Protein/peptide | Mass: 977.975 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: This sequence occurs naturally in Homo sapiens (humans) References: UniProt: P05067*PLUS |
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-Antibody , 2 types, 4 molecules LKHG
#1: Antibody | Mass: 24146.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: hybridoma / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c / References: UniProt: A2NHM3*PLUS #2: Antibody | Mass: 24095.115 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: hybridoma / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c |
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-Non-polymers , 3 types, 127 molecules
#4: Chemical | #5: Chemical | ChemComp-GOL / #6: 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: 2.17 Å3/Da / Density % sol: 43.29 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 8.5 Details: 0.1 M Tris, 25% PEG3350, pH 8.5, VAPOR DIFFUSION, temperature 294K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 20, 2006 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→23.53 Å / Num. obs: 90408 / % possible obs: 90.7 % / Redundancy: 3.1 % / Rsym value: 0.055 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.467 / % possible all: 66.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2IQ9 Resolution: 1.65→23.53 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.106 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 14.361 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→23.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.69 Å / Total num. of bins used: 20
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