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Yorodumi- PDB-3gci: Crystal Structure of the Complex Formed Between a New Isoform of ... -
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-Basic information
Entry | Database: PDB / ID: 3gci | ||||||
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Title | Crystal Structure of the Complex Formed Between a New Isoform of Phospholipase A2 with C-terminal Amyloid Beta Heptapeptide at 2 A Resolution | ||||||
Components |
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Keywords | HYDROLASE / PHOSPHOLIPASE A2 / HEPTAPEPTIDE / AMYLOID BETA / Lipid degradation / Metal-binding / Secreted | ||||||
Function / homology | Function and homology information 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 / synaptic assembly at neuromuscular junction / Formyl peptide receptors bind formyl peptides and many other ligands / signaling receptor activator activity ...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 / synaptic assembly at neuromuscular junction / Formyl peptide receptors bind formyl peptides and many other ligands / signaling receptor activator activity / phospholipase A2 / axon midline choice point recognition / smooth endoplasmic reticulum calcium ion homeostasis / calcium-dependent phospholipase A2 activity / astrocyte activation involved in immune response / regulation of spontaneous synaptic transmission / mating behavior / Lysosome Vesicle Biogenesis / ciliary rootlet / PTB domain binding / arachidonate secretion / 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 / phospholipid metabolic process / lipid catabolic process / clathrin-coated pit / protein serine/threonine kinase binding / regulation of peptidyl-tyrosine phosphorylation / positive regulation of chemokine production / 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 / 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 / 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 / recycling endosome / phospholipid binding / 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 / endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cellular response to amyloid-beta / positive regulation of tumor necrosis factor production Similarity search - Function | ||||||
Biological species | Naja sagittifera (cobra) HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.04 Å | ||||||
Authors | Mirza, Z. / Vikram, G. / Singh, N. / Sinha, M. / Bhushan, A. / Sharma, S. / Srinivasan, A. / Kaur, P. / Singh, T.P. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Complex Formed Between a New Isoform of Phospholipase A2 with C-terminal Amyloid Beta Heptapeptide at 2 A Resolution Authors: Mirza, Z. / Vikram, G. / Singh, N. / Sinha, M. / Bhushan, A. / Sharma, S. / Srinivasan, A. / Kaur, P. / Singh, T.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gci.cif.gz | 40.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gci.ent.gz | 26.5 KB | Display | PDB format |
PDBx/mmJSON format | 3gci.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gci_validation.pdf.gz | 431.7 KB | Display | wwPDB validaton report |
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Full document | 3gci_full_validation.pdf.gz | 432.3 KB | Display | |
Data in XML | 3gci_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 3gci_validation.cif.gz | 10.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gc/3gci ftp://data.pdbj.org/pub/pdb/validation_reports/gc/3gci | HTTPS FTP |
-Related structure data
Related structure data | 1mf4S 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: 13094.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Naja sagittifera (cobra) / References: UniProt: P60045, phospholipase A2 |
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#2: Protein/peptide | Mass: 613.747 Da / Num. of mol.: 1 / Fragment: UNP residues 707-713 / Source method: obtained synthetically Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. This sequence occurs naturally in humans. Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P05067 |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
Sequence details | IN CHAIN A, RESIDUE NUMBER 16 IS SIMPLY SKIPPED. THE AUTHORS BELIEVE THAT THE SEQRES IS CORRECT AND ...IN CHAIN A, RESIDUE NUMBER 16 IS SIMPLY SKIPPED. THE AUTHORS BELIEVE THAT THE SEQRES IS CORRECT AND THESE MUTATIONS ARE PRESENT IN THE DEPOSITED SEQUENCE. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.74 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 10mM Sodium phosphate, pH 6.0, 1mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 23, 2008 / Details: MIRROR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→20 Å / Num. all: 7596 / Num. obs: 7596 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.115 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.04→2.09 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.305 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MF4 Resolution: 2.04→19.51 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.618 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.232 / ESU R Free: 0.178 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.418 Å2
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Refinement step | Cycle: LAST / Resolution: 2.04→19.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.04→2.092 Å / Total num. of bins used: 20
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