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Yorodumi- PDB-4nge: Crystal Structure of Human Presequence Protease in Complex with A... -
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-Basic information
Entry | Database: PDB / ID: 4nge | ||||||
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Title | Crystal Structure of Human Presequence Protease in Complex with Amyloid-beta (1-40) | ||||||
Components |
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Keywords | HYDROLASE/PROTEIN BINDING / M16 metalloprotease / Alzheimer's disease / zinc metalloendoprotease / monomethyllysine / dimethyllysine / S-(dimethylarsenic)cysteine / mitochondrial matrix / HYDROLASE-PROTEIN BINDING complex | ||||||
Function / homology | Function and homology information Mitochondrial protein import / protein targeting to mitochondrion / regulation of epidermal growth factor-activated receptor activity / signaling receptor activator activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases ...Mitochondrial protein import / protein targeting to mitochondrion / regulation of epidermal growth factor-activated receptor activity / signaling receptor activator activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / Formyl peptide receptors bind formyl peptides and many other ligands / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / 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 / regulation of Wnt signaling pathway / mating behavior / positive regulation of amyloid fibril formation / ciliary rootlet / Lysosome Vesicle Biogenesis / PTB domain binding / Golgi-associated vesicle / neuron remodeling / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / : / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / presynaptic active zone / nuclear envelope lumen / modulation of excitatory postsynaptic potential / suckling behavior / COPII-coated ER to Golgi transport vesicle / dendrite development / smooth endoplasmic reticulum / regulation of NMDA receptor activity / TRAF6 mediated NF-kB activation / negative regulation of long-term synaptic potentiation / Advanced glycosylation endproduct receptor signaling / neuromuscular process controlling balance / regulation of presynapse assembly / The NLRP3 inflammasome / intracellular copper ion homeostasis / transition metal ion binding / regulation of multicellular organism growth / enzyme activator activity / negative regulation of neuron differentiation / ECM proteoglycans / spindle midzone / positive regulation of T cell migration / Purinergic signaling in leishmaniasis infection / positive regulation of calcium-mediated signaling / forebrain development / regulation of peptidyl-tyrosine phosphorylation / positive regulation of chemokine production / clathrin-coated pit / Notch signaling pathway / cholesterol metabolic process / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of protein metabolic process / ionotropic glutamate receptor signaling pathway / neuron projection maintenance / positive regulation of glycolytic process / extracellular matrix organization / positive regulation of mitotic cell cycle / response to interleukin-1 / axonogenesis / adult locomotory behavior / trans-Golgi network membrane / dendritic shaft / locomotory behavior / platelet alpha granule lumen / 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 / astrocyte activation / endosome lumen / Post-translational protein phosphorylation / synapse organization / microglial cell activation / regulation of long-term neuronal synaptic plasticity / positive regulation of JNK cascade / TAK1-dependent IKK and NF-kappa-B activation / neuromuscular junction / visual learning / serine-type endopeptidase inhibitor activity / metalloendopeptidase activity / protein processing / recycling endosome / cognition / positive regulation of inflammatory response / positive regulation of interleukin-6 production / neuron cellular homeostasis / Golgi lumen / endocytosis / positive regulation of non-canonical NF-kappaB signal transduction / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / neuron projection development / cellular response to amyloid-beta Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / molecular replacement/SAD / Resolution: 2.704 Å | ||||||
Authors | King, J.V. / Liang, W.G. / Tang, W.J. | ||||||
Citation | Journal: Structure / Year: 2014 Title: Molecular basis of substrate recognition and degradation by human presequence protease. Authors: King, J.V. / Liang, W.G. / Scherpelz, K.P. / Schilling, A.B. / Meredith, S.C. / Tang, W.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nge.cif.gz | 411.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nge.ent.gz | 338.7 KB | Display | PDB format |
PDBx/mmJSON format | 4nge.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ng/4nge ftp://data.pdbj.org/pub/pdb/validation_reports/ng/4nge | HTTPS FTP |
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-Related 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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-Components
-Presequence protease, ... , 2 types, 2 molecules AD
#1: Protein | Mass: 115762.133 Da / Num. of mol.: 1 / Fragment: UNP residues 33-1037 / Mutation: E107Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA1104, MP1, PITRM1 / Plasmid: pProExH6 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) References: UniProt: Q5JRX3, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases |
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#4: Protein | Mass: 115572.414 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 Source method: isolated from a genetically manipulated source Source: (synth.) Homo sapiens (human) / References: UniProt: Q5JRX3 |
-Beta-amyloid protein ... , 2 types, 4 molecules BECF
#2: Protein/peptide | Mass: 4335.852 Da / Num. of mol.: 2 / Fragment: UNP residues 572-711 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P05067 #3: Protein/peptide | Mass: 613.749 Da / Num. of mol.: 2 / Fragment: UNP residues 33-1037 / Mutation: E107Q / Source method: obtained synthetically / Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA1104, MP1, PITRM1 / Plasmid: pProExH6 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) References: Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases |
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-Non-polymers , 4 types, 47 molecules
#5: Chemical | #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | I328V, A397V, AND Q1037R IN CHAINS A AND D ARE NATURAL VARIANTS. CHAINS C AND F ARE IDENTICAL TO ...I328V, A397V, AND Q1037R IN CHAINS A AND D ARE NATURAL VARIANTS. CHAINS C AND F ARE IDENTICAL TO CHAINS B AND E, BUT THE IDENTITIES |
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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: 2.78 Å3/Da / Density % sol: 55.71 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 15.2% w/v PEG8000, 15 mM TCEP, 80 mM sodium cacodylate, pH 6.5, 160 mM calcium acetate, 20% v/v glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K |
-Data collection
Diffraction | Mean temperature: 113.5 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.045 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2013 |
Radiation | Monochromator: Rosenbaum-Rock high-resolution double-crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.045 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 72669 / Num. obs: 67540 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 36.28 Å2 / Rsym value: 0.18 / Net I/σ(I): 8.69 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.75 / Num. unique all: 3557 / Rsym value: 0.597 / % possible all: 98.2 |
-Processing
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Refinement | Method to determine structure: molecular replacement/SAD / Resolution: 2.704→39.621 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 24.7 / Stereochemistry target values: MLHL Details: THE PRESENCE IN THE ASYMMETRIC UNIT OF TWO PROTEINS (CHAINS A AND D) WITH DISTINCT PATTERNS OF SIDE CHAIN MODIFICATION REPRESENTS THE BEST FIT TO THE ELECTRON DENSITY AND IS NOT DERIVED FROM ...Details: THE PRESENCE IN THE ASYMMETRIC UNIT OF TWO PROTEINS (CHAINS A AND D) WITH DISTINCT PATTERNS OF SIDE CHAIN MODIFICATION REPRESENTS THE BEST FIT TO THE ELECTRON DENSITY AND IS NOT DERIVED FROM THE CO-CRYSTALLIZATION OF TWO CHEMICALLY DISTINCT PROTEINS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.63 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.704→39.621 Å
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Refine LS restraints |
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LS refinement shell |
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