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Yorodumi- PDB-3ejh: Crystal Structure of the Fibronectin 8-9FnI Domain Pair in Comple... -
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-Basic information
Entry | Database: PDB / ID: 3ejh | ||||||
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Title | Crystal Structure of the Fibronectin 8-9FnI Domain Pair in Complex with a Type-I Collagen Peptide | ||||||
Components |
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Keywords | CELL ADHESION / fibronectin / collagen / protein complex / collagenase site / Acute phase / Disease mutation / Extracellular matrix / Glycoprotein / Heparin-binding / Phosphoprotein / Pyrrolidone carboxylic acid / Secreted / Sulfation | ||||||
Function / homology | Function and homology information negative regulation of monocyte activation / calcium-independent cell-matrix adhesion / negative regulation of transforming growth factor beta production / Fibronectin matrix formation / Extracellular matrix organization / 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 ...negative regulation of monocyte activation / calcium-independent cell-matrix adhesion / negative regulation of transforming growth factor beta production / Fibronectin matrix formation / Extracellular matrix organization / 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 / biological process involved in interaction with symbiont / Molecules associated with elastic fibres / proteoglycan binding / MET activates PTK2 signaling / extracellular matrix structural constituent / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / endodermal cell differentiation / GRB2:SOS provides linkage to MAPK signaling for Integrins / endoplasmic reticulum-Golgi intermediate compartment / Non-integrin membrane-ECM interactions / basement membrane / ECM proteoglycans / Integrin cell surface interactions / positive regulation of axon extension / collagen binding / Degradation of the extracellular matrix / Integrin signaling / substrate adhesion-dependent cell spreading / regulation of ERK1 and ERK2 cascade / cell-matrix adhesion / extracellular matrix / platelet alpha granule lumen / acute-phase response / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / Post-translational protein phosphorylation / regulation of protein phosphorylation / Signaling by high-kinase activity BRAF mutants / wound healing / MAP2K and MAPK activation / response to wounding / GPER1 signaling / 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 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Signaling by BRAF and RAF1 fusions / positive regulation of fibroblast proliferation / Signaling by ALK fusions and activated point mutants / integrin binding / Platelet degranulation / nervous system development / heparin binding / heart development / regulation of cell shape / angiogenesis / Interleukin-4 and Interleukin-13 signaling / collagen-containing extracellular matrix / protease binding / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / blood microparticle / cell adhesion / apical plasma membrane / endoplasmic reticulum lumen / signaling receptor binding / positive regulation of cell population proliferation / 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 / Resolution: 2.1 Å | ||||||
Authors | Erat, M.C. / Lowe, E.D. / Campbell, I.D. / Vakonakis, I. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Identification and structural analysis of type I collagen sites in complex with fibronectin fragments. Authors: Erat, M.C. / Slatter, D.A. / Lowe, E.D. / Millard, C.J. / Farndale, R.W. / Campbell, I.D. / Vakonakis, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ejh.cif.gz | 112.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ejh.ent.gz | 87.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ejh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ejh_validation.pdf.gz | 485.1 KB | Display | wwPDB validaton report |
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Full document | 3ejh_full_validation.pdf.gz | 489.1 KB | Display | |
Data in XML | 3ejh_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 3ejh_validation.cif.gz | 16.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/3ejh ftp://data.pdbj.org/pub/pdb/validation_reports/ej/3ejh | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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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: 10891.985 Da / Num. of mol.: 2 / Fragment: 8-9FnI / Mutation: N528Q, R534K Source method: isolated from a genetically manipulated source Details: Integration in the AOX1 locus / Source: (gene. exp.) Homo sapiens (human) / Gene: FN1, FN / Production host: Pichia pastoris (fungus) / Strain (production host): X-33 / References: UniProt: P02751 #2: Protein/peptide | Mass: 2405.651 Da / Num. of mol.: 2 / Fragment: collagenase site C-terminal peptide / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human) type-I collagen a1 chain. #3: Sugar | #4: Chemical | ChemComp-GOL / | #5: 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: 2.63 Å3/Da / Density % sol: 53.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 2.5 M NaCl, 0.1 M BisTris pH 6.5 , VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 28, 2008 |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2→49.225 Å / Num. obs: 19940 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 40.9 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 6.023 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 1.2 / Num. measured all: 20451 / Num. unique all: 2872 / Rsym value: 0.571 / % possible all: 100 |
-Processing
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Refinement | Starting model: PDB ENTRIES 2CG6, 2CG7 Resolution: 2.1→49.225 Å / Occupancy max: 1 / Occupancy min: 0.29 / FOM work R set: 0.828 / SU ML: 0.33 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.4 / Stereochemistry target values: ML / Details: One TLS group per FnI domain and peptide chain
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.312 Å2 / ksol: 0.375 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 144.75 Å2 / Biso mean: 52.401 Å2 / Biso min: 20.1 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→49.225 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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