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Yorodumi- PDB-5n47: Structure of Anticalin N7E in complex with the three-domain fragm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5n47 | ||||||
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Title | Structure of Anticalin N7E in complex with the three-domain fragment Fn7B8 of human oncofetal fibronectin | ||||||
Components |
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Keywords | PROTEIN BINDING / LIPOCALIN / ANTICALIN / LIPOCALIN-BASED BINDING PROTEIN / HUMAN FIBRONECTIN / ONCOFETAL SPLICE VARIANT / FN TYPE III DOMAIN / EXTRA-DOMAIN B / EIIIB / ED-B / EXTRACELLULAR MATRIX / STRUCTURAL PROTEIN | ||||||
Function / homology | Function and homology information negative regulation of monocyte activation / calcium-independent cell-matrix adhesion / negative regulation of transforming growth factor beta production / siderophore transport / Fibronectin matrix formation / Extracellular matrix organization / Metal sequestration by antimicrobial proteins / positive regulation of substrate-dependent cell migration, cell attachment to substrate / neural crest cell migration involved in autonomic nervous system development / peptidase activator activity ...negative regulation of monocyte activation / calcium-independent cell-matrix adhesion / negative regulation of transforming growth factor beta production / siderophore transport / Fibronectin matrix formation / Extracellular matrix organization / Metal sequestration by antimicrobial proteins / positive regulation of substrate-dependent cell migration, cell attachment to substrate / neural crest cell migration involved in autonomic nervous system development / peptidase activator activity / fibrinogen complex / peptide cross-linking / integrin activation / ALK mutants bind TKIs / cell-substrate junction assembly / iron ion sequestering activity / enterobactin binding / biological process involved in interaction with symbiont / Molecules associated with elastic fibres / proteoglycan binding / extracellular matrix structural constituent / MET activates PTK2 signaling / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / endodermal cell differentiation / small molecule binding / GRB2:SOS provides linkage to MAPK signaling for Integrins / Non-integrin membrane-ECM interactions / Signaling by ALK fusions and activated point mutants / basement membrane / ECM proteoglycans / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of axon extension / Integrin cell surface interactions / Nuclear events stimulated by ALK signaling in cancer / collagen binding / extracellular matrix / Degradation of the extracellular matrix / Integrin signaling / substrate adhesion-dependent cell spreading / cell-matrix adhesion / regulation of ERK1 and ERK2 cascade / platelet alpha granule lumen / integrin-mediated signaling pathway / Post-translational protein phosphorylation / acute-phase response / Cell surface interactions at the vascular wall / Iron uptake and transport / regulation of protein phosphorylation / Signaling by high-kinase activity BRAF mutants / wound healing / MAP2K and MAPK activation / response to wounding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / GPER1 signaling / specific granule lumen / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / positive regulation of fibroblast proliferation / Signaling by BRAF and RAF1 fusions / integrin binding / Platelet degranulation / heparin binding / nervous system development / positive regulation of cold-induced thermogenesis / heart development / regulation of cell shape / collagen-containing extracellular matrix / angiogenesis / blood microparticle / Interleukin-4 and Interleukin-13 signaling / protease binding / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / defense response to bacterium / iron ion binding / apical plasma membrane / endoplasmic reticulum lumen / signaling receptor binding / innate immune response / apoptotic process / positive regulation of cell population proliferation / Neutrophil degranulation / positive regulation of gene expression / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Schiefner, A. / Skerra, A. | ||||||
Citation | Journal: Structure / Year: 2018 Title: Anticalins Reveal High Plasticity in the Mode of Complex Formation with a Common Tumor Antigen. Authors: Schiefner, A. / Gebauer, M. / Richter, A. / Skerra, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n47.cif.gz | 512.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n47.ent.gz | 426.4 KB | Display | PDB format |
PDBx/mmJSON format | 5n47.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n4/5n47 ftp://data.pdbj.org/pub/pdb/validation_reports/n4/5n47 | HTTPS FTP |
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-Related structure data
Related structure data | 5n48C 4gh7S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 21727.689 Da / Num. of mol.: 3 Mutation: Q28H, L36E, A40S, I41L, Q49R, L70R, K73S, D77H, W79L, C87S, N96L, Y100K, L103H, Y106F, K125T, S127A, K134F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LCN2, HNL, NGAL / Plasmid: pNGAL98-N7E Production host: Escherichia coli str. K-12 substr. W3110 (bacteria) References: UniProt: P80188 #2: Protein | Mass: 30834.922 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FN1, FN / Plasmid: pASK75-Fn7B8-His / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P02751 |
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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: 58.34 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 17 % (w/v) PEG3350, 0.2 M NaCl, 0.1 M Na-malonate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 24, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→35 Å / Num. obs: 38486 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 14.67 % / Biso Wilson estimate: 63.078 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.124 / Rrim(I) all: 0.129 / Χ2: 1.022 / Net I/σ(I): 21.7 / Num. measured all: 564576 / Scaling rejects: 168 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GH7 Resolution: 3→35 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.902 / SU B: 37.802 / SU ML: 0.304 / SU R Cruickshank DPI: 0.3714 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.384 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 240.24 Å2 / Biso mean: 97.772 Å2 / Biso min: 37.46 Å2
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Refinement step | Cycle: final / Resolution: 3→35 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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