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Yorodumi- PDB-5jxi: Structure of the unliganded form of the proprotein convertase fur... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jxi | |||||||||
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Title | Structure of the unliganded form of the proprotein convertase furin in presence of EDTA. | |||||||||
Components | Furin | |||||||||
Keywords | HYDROLASE / protease / apo-structure / proteolysis | |||||||||
Function / homology | Function and homology information furin / nerve growth factor production / dibasic protein processing / plasma lipoprotein particle remodeling / NGF processing / Assembly of active LPL and LIPC lipase complexes / negative regulation of transforming growth factor beta1 production / signal peptide processing / regulation of cholesterol transport / negative regulation of low-density lipoprotein particle receptor catabolic process ...furin / nerve growth factor production / dibasic protein processing / plasma lipoprotein particle remodeling / NGF processing / Assembly of active LPL and LIPC lipase complexes / negative regulation of transforming growth factor beta1 production / signal peptide processing / regulation of cholesterol transport / negative regulation of low-density lipoprotein particle receptor catabolic process / peptide biosynthetic process / cytokine precursor processing / Pre-NOTCH Processing in Golgi / secretion by cell / Synthesis and processing of ENV and VPU / Formation of the cornified envelope / nerve growth factor binding / Signaling by PDGF / trans-Golgi network transport vesicle / Elastic fibre formation / heparan sulfate binding / Signaling by NODAL / blastocyst formation / Respiratory syncytial virus (RSV) attachment and entry / regulation of endopeptidase activity / positive regulation of membrane protein ectodomain proteolysis / peptide hormone processing / zymogen activation / CD163 mediating an anti-inflammatory response / regulation of protein catabolic process / Activation of Matrix Metalloproteinases / Maturation of hRSV A proteins / TGF-beta receptor signaling activates SMADs / Uptake and function of anthrax toxins / Collagen degradation / protein maturation / collagen catabolic process / extracellular matrix disassembly / regulation of signal transduction / Removal of aminoterminal propeptides from gamma-carboxylated proteins / negative regulation of inflammatory response to antigenic stimulus / viral life cycle / serine-type peptidase activity / transforming growth factor beta receptor signaling pathway / extracellular matrix organization / peptide binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / trans-Golgi network / protein processing / Golgi lumen / serine-type endopeptidase inhibitor activity / heparin binding / peptidase activity / endopeptidase activity / Potential therapeutics for SARS / protease binding / viral translation / amyloid fibril formation / Induction of Cell-Cell Fusion / Attachment and Entry / endosome membrane / positive regulation of viral entry into host cell / viral protein processing / membrane raft / Amyloid fiber formation / Golgi membrane / serine-type endopeptidase activity / cell surface / endoplasmic reticulum / extracellular exosome / extracellular region / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Dahms, S.O. / Arciniega, M. / Steinmetzer, T. / Huber, R. / Than, M.E. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Structure of the unliganded form of the proprotein convertase furin suggests activation by a substrate-induced mechanism. Authors: Dahms, S.O. / Arciniega, M. / Steinmetzer, T. / Huber, R. / Than, M.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jxi.cif.gz | 121.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jxi.ent.gz | 90.3 KB | Display | PDB format |
PDBx/mmJSON format | 5jxi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jxi_validation.pdf.gz | 425.8 KB | Display | wwPDB validaton report |
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Full document | 5jxi_full_validation.pdf.gz | 426 KB | Display | |
Data in XML | 5jxi_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | 5jxi_validation.cif.gz | 35.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jx/5jxi ftp://data.pdbj.org/pub/pdb/validation_reports/jx/5jxi | HTTPS FTP |
-Related structure data
Related structure data | 5jxgC 5jxhC 5jxjC 4rydS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 52388.602 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FURIN, FUR, PACE, PCSK3 / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P09958, furin | ||||
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#2: Chemical | ChemComp-CA / | ||||
#3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-CL / | #5: 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: 3.76 Å3/Da / Density % sol: 67.3 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: crystallization solution: 100 mM MES, 200 mM K/NaH2PO4, pH 5.5-6.0, 3-4 M NaCl, 3% DMSO; reservoir solution: 3-4 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918409 Å / Relative weight: 1 |
Reflection | Resolution: 2→46.2 Å / Num. obs: 54336 / % possible obs: 98.9 % / Redundancy: 4.9 % / Rsym value: 0.116 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2→2.12 Å / Rsym value: 0.595 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4RYD Resolution: 2→43.354 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.03
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→43.354 Å
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Refine LS restraints |
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LS refinement shell |
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