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Yorodumi- PDB-5jmo: X-ray structure of furin in complex with the inhibitory antibody Nb14 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jmo | ||||||
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Title | X-ray structure of furin in complex with the inhibitory antibody Nb14 | ||||||
Components |
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Keywords | Hydrolase/Antibody / protease / camelid / antibody / complex / Hydrolase-Antibody complex / furin | ||||||
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 / regulation of endopeptidase activity / positive regulation of membrane protein ectodomain proteolysis / zymogen activation / peptide hormone processing / 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 / Respiratory syncytial virus (RSV) attachment and entry / Uptake and function of anthrax toxins / protein maturation / Collagen degradation / 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 / extracellular matrix organization / transforming growth factor beta receptor signaling pathway / peptide binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / serine-type endopeptidase inhibitor activity / trans-Golgi network / protein processing / Golgi lumen / peptidase activity / heparin binding / protease binding / endopeptidase activity / viral translation / amyloid fibril formation / Potential therapeutics for SARS / Induction of Cell-Cell Fusion / Attachment and Entry / positive regulation of viral entry into host cell / viral protein processing / endosome membrane / 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) Camelus dromedarius (Arabian camel) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.998 Å | ||||||
Authors | Dahms, S.O. / Than, M.E. | ||||||
Citation | Journal: Sci Rep / Year: 2016 Title: The structure of a furin-antibody complex explains non-competitive inhibition by steric exclusion of substrate conformers. Authors: Dahms, S.O. / Creemers, J.W. / Schaub, Y. / Bourenkov, G.P. / Zogg, T. / Brandstetter, H. / 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 | 5jmo.cif.gz | 260.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jmo.ent.gz | 203.4 KB | Display | PDB format |
PDBx/mmJSON format | 5jmo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jmo_validation.pdf.gz | 483.5 KB | Display | wwPDB validaton report |
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Full document | 5jmo_full_validation.pdf.gz | 492.2 KB | Display | |
Data in XML | 5jmo_validation.xml.gz | 49.1 KB | Display | |
Data in CIF | 5jmo_validation.cif.gz | 72.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jm/5jmo ftp://data.pdbj.org/pub/pdb/validation_reports/jm/5jmo | HTTPS FTP |
-Related structure data
Related structure data | 5jmrSC 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein / Antibody / Protein/peptide / Sugars , 4 types, 10 molecules ABCDGH
#1: Protein | Mass: 52388.602 Da / Num. of mol.: 2 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 #2: Antibody | Mass: 12615.001 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli (E. coli) #3: Protein/peptide | #4: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 777 molecules
#5: Chemical | ChemComp-CA / #6: Chemical | #7: 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: 2.33 Å3/Da / Density % sol: 47.2 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: .1 M sodium acetate, pH 5.6, 16-18% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.998→66.381 Å / Num. obs: 83341 / % possible obs: 98.8 % / Redundancy: 6.73 % / Rsym value: 0.132 / Net I/σ(I): 12.02 |
Reflection shell | Resolution: 1.998→2.12 Å / Rsym value: 0.608 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4RYD (furin, chain A or chain B) and 5JMR (antibody, chain C or chain D) Resolution: 1.998→66.381 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.21 / Phase error: 17.91 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.998→66.381 Å
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Refine LS restraints |
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LS refinement shell |
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