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Yorodumi- PDB-5am8: Crystal structure of the Angiotensin-1 converting enzyme N-domain... -
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-Basic information
Entry | Database: PDB / ID: 5am8 | |||||||||
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Title | Crystal structure of the Angiotensin-1 converting enzyme N-domain in complex with amyloid-beta 4-10 | |||||||||
Components |
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Keywords | HYDROLASE / METALLOPROTEASE / AMYLOID-BETA | |||||||||
Function / homology | Function and homology information mononuclear cell proliferation / cell proliferation in bone marrow / bradykinin receptor binding / regulation of angiotensin metabolic process / exopeptidase activity / substance P catabolic process / peptidyl-dipeptidase A / tripeptidyl-peptidase activity / regulation of renal output by angiotensin / negative regulation of calcium ion import ...mononuclear cell proliferation / cell proliferation in bone marrow / bradykinin receptor binding / regulation of angiotensin metabolic process / exopeptidase activity / substance P catabolic process / peptidyl-dipeptidase A / tripeptidyl-peptidase activity / regulation of renal output by angiotensin / negative regulation of calcium ion import / positive regulation of peptidyl-cysteine S-nitrosylation / response to laminar fluid shear stress / negative regulation of gap junction assembly / metallodipeptidase activity / positive regulation of systemic arterial blood pressure / cellular response to aldosterone / hormone catabolic process / bradykinin catabolic process / angiogenesis involved in coronary vascular morphogenesis / response to thyroid hormone / antigen processing and presentation of peptide antigen via MHC class I / negative regulation of glucose import / vasoconstriction / regulation of epidermal growth factor-activated receptor activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / hormone metabolic process / neutrophil mediated immunity / microglia development / regulation of smooth muscle cell migration / regulation of hematopoietic stem cell proliferation / 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 / 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 / mitogen-activated protein kinase binding / embryo development ending in birth or egg hatching / chloride ion binding / ciliary rootlet / mitogen-activated protein kinase kinase binding / positive regulation of neurogenesis / Lysosome Vesicle Biogenesis / PTB domain binding / Golgi-associated vesicle / arachidonic acid secretion / post-transcriptional regulation of gene expression / eating behavior / positive regulation of amyloid fibril formation / neuron remodeling / : / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / heterocyclic compound binding / lung alveolus development / heart contraction / peptide catabolic process / suckling behavior / nuclear envelope lumen / response to dexamethasone / dendrite development / COPII-coated ER to Golgi transport vesicle / presynaptic active zone / regulation of heart rate by cardiac conduction / modulation of excitatory postsynaptic potential / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / regulation of systemic arterial blood pressure by renin-angiotensin / neuromuscular process controlling balance / The NLRP3 inflammasome / regulation of presynapse assembly / transition metal ion binding / negative regulation of long-term synaptic potentiation / regulation of multicellular organism growth / intracellular copper ion homeostasis / negative regulation of neuron differentiation / regulation of vasoconstriction / ECM proteoglycans / smooth endoplasmic reticulum / peptidyl-dipeptidase activity / hematopoietic stem cell differentiation / positive regulation of T cell migration / blood vessel remodeling / spindle midzone / angiotensin maturation / amyloid-beta metabolic process / animal organ regeneration / Metabolism of Angiotensinogen to Angiotensins / Purinergic signaling in leishmaniasis infection / positive regulation of calcium-mediated signaling / protein serine/threonine kinase binding / positive regulation of chemokine production / clathrin-coated pit Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Masuyer, G. / Larmuth, K.M. / Douglas, R.G. / Sturrock, E.D. / Acharya, K.R. | |||||||||
Citation | Journal: FEBS J. / Year: 2016 Title: The Kinetic and Structural Characterisation of Amyloid-Beta Metabolism by Human Angiotensin-1- Converting Enzyme (Ace) Authors: Larmuth, K.M. / Masuyer, G. / Douglas, R.G. / Sturrock, E.D. / Acharya, K.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5am8.cif.gz | 1010.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5am8.ent.gz | 844 KB | Display | PDB format |
PDBx/mmJSON format | 5am8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5am8_validation.pdf.gz | 3.9 MB | Display | wwPDB validaton report |
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Full document | 5am8_full_validation.pdf.gz | 3.9 MB | Display | |
Data in XML | 5am8_validation.xml.gz | 103.4 KB | Display | |
Data in CIF | 5am8_validation.cif.gz | 153.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/5am8 ftp://data.pdbj.org/pub/pdb/validation_reports/am/5am8 | HTTPS FTP |
-Related structure data
Related structure data | 5am9C 5amaC 5ambC 5amcC 3nxqS 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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3 |
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4 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 8 molecules ABCDPQRS
#1: Protein | Mass: 72592.477 Da / Num. of mol.: 4 / Fragment: N DOMAIN, UNP RESIDUES 30-658 / Mutation: YES Source method: isolated from a genetically manipulated source Details: MINIMALLY GLYCOSYLATED MUTANT / Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): CHO K1 / Production host: CRICETULUS GRISEUS (Chinese hamster) References: UniProt: P12821, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds, peptidyl-dipeptidase A #2: Protein/peptide | Mass: 882.921 Da / Num. of mol.: 4 / Fragment: FRAGMENT 4-10, UNP RESIDUES 675-681 / Source method: obtained synthetically / Details: ONLY DI-PEPTIDE ASP-SER (7-8) VISIBLE IN STRUCTURE / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P05067 |
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-Sugars , 6 types, 12 molecules
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6) ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #7: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #11: Sugar | |
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-Non-polymers , 6 types, 1862 molecules
#8: Chemical | ChemComp-ZN / #9: Chemical | ChemComp-CL / #10: Chemical | ChemComp-SO4 / #12: Chemical | ChemComp-PEG / #13: Chemical | #14: Water | ChemComp-HOH / | |
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-Details
Sequence details | MINIMALLY GLYCOSYLAT |
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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: 2.95 Å3/Da / Density % sol: 58 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 0.06 M DIVALENT CATIONS, 0.1 M TRIS/BICINE PH 8.5, 30 % PEG550MME/PEG20000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→113.8 Å / Num. obs: 293455 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 1.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.4 / % possible all: 84 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3NXQ Resolution: 1.9→113.78 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.757 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ONLY RESIDUES 7-8 OF AMYLOID-BETA 4-10 WERE VISIBLE
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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: 25.005 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→113.78 Å
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