+Open data
-Basic information
Entry | Database: PDB / ID: 5jz7 | ||||||
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Title | NGF IN COMPLEX WITH MEDI578 scFv | ||||||
Components |
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Keywords | SIGNALING PROTEIN / Antibody / complex / epitope / NGF | ||||||
Function / homology | Function and homology information NFG and proNGF binds to p75NTR / Ceramide signalling / nerve growth factor receptor binding / NGF processing / TRKA activation by NGF / PLC-gamma1 signalling / Signalling to STAT3 / p75NTR negatively regulates cell cycle via SC1 / metalloendopeptidase inhibitor activity / nerve growth factor signaling pathway ...NFG and proNGF binds to p75NTR / Ceramide signalling / nerve growth factor receptor binding / NGF processing / TRKA activation by NGF / PLC-gamma1 signalling / Signalling to STAT3 / p75NTR negatively regulates cell cycle via SC1 / metalloendopeptidase inhibitor activity / nerve growth factor signaling pathway / nerve development / Retrograde neurotrophin signalling / Axonal growth stimulation / positive regulation of collateral sprouting / NADE modulates death signalling / Signalling to p38 via RIT and RIN / peripheral nervous system development / ARMS-mediated activation / positive regulation of Ras protein signal transduction / PI3K/AKT activation / regulation of neuron differentiation / Frs2-mediated activation / NRAGE signals death through JNK / extrinsic apoptotic signaling pathway via death domain receptors / Signalling to RAS / positive regulation of DNA binding / p75NTR recruits signalling complexes / positive regulation of neuron differentiation / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / neuron projection morphogenesis / endosome lumen / cell surface receptor protein tyrosine kinase signaling pathway / growth factor activity / modulation of chemical synaptic transmission / memory / Golgi lumen / synaptic vesicle / positive regulation of peptidyl-serine phosphorylation / negative regulation of neuron apoptotic process / negative regulation of cell population proliferation / axon / lipid binding / dendrite / positive regulation of gene expression / extracellular space / extracellular region / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Olsson, L.-L. / Aagaard, A. | ||||||
Citation | Journal: Sci Rep / Year: 2016 Title: Engineering the surface properties of a human monoclonal antibody prevents self-association and rapid clearance in vivo. Authors: Dobson, C.L. / Devine, P.W. / Phillips, J.J. / Higazi, D.R. / Lloyd, C. / Popovic, B. / Arnold, J. / Buchanan, A. / Lewis, A. / Goodman, J. / van der Walle, C.F. / Thornton, P. / Vinall, L. ...Authors: Dobson, C.L. / Devine, P.W. / Phillips, J.J. / Higazi, D.R. / Lloyd, C. / Popovic, B. / Arnold, J. / Buchanan, A. / Lewis, A. / Goodman, J. / van der Walle, C.F. / Thornton, P. / Vinall, L. / Lowne, D. / Aagaard, A. / Olsson, L.L. / Ridderstad Wollberg, A. / Welsh, F. / Karamanos, T.K. / Pashley, C.L. / Iadanza, M.G. / Ranson, N.A. / Ashcroft, A.E. / Kippen, A.D. / Vaughan, T.J. / Radford, S.E. / Lowe, D.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jz7.cif.gz | 265 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jz7.ent.gz | 216.1 KB | Display | PDB format |
PDBx/mmJSON format | 5jz7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jz/5jz7 ftp://data.pdbj.org/pub/pdb/validation_reports/jz/5jz7 | 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
#1: Protein | Mass: 12421.160 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NGF, NGFB / Plasmid: PET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01138 #2: Antibody | Mass: 13970.527 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #3: Antibody | Mass: 12695.915 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
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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: 3.01 Å3/Da / Density % sol: 59.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 18 % PEG 8000, 150 mM NaCl, 100 mM MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 18, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→47.02 Å / Num. obs: 24799 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 39.87 Å2 / Rmerge(I) obs: 0.37 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 3.4→3.49 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 1.9 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BTG, 1AQK Resolution: 3.4→47.02 Å / Cor.coef. Fo:Fc: 0.823 / Cor.coef. Fo:Fc free: 0.8069 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.57
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Displacement parameters | Biso mean: 56.88 Å2
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Refine analyze | Luzzati coordinate error obs: 0.804 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.4→47.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.4→3.55 Å / Total num. of bins used: 12
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