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- PDB-3gxe: Complex of a Low Affinity Collagen Site with the Fibronectin 8-9F... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3gxe | ||||||
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Title | Complex of a Low Affinity Collagen Site with the Fibronectin 8-9FnI Domain Pair | ||||||
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![]() | CELL ADHESION / protein-peptide complex | ||||||
Function / homology | ![]() cellular response to fluoride / collagen type I trimer / tooth mineralization / cellular response to vitamin E / collagen type IV trimer / Anchoring fibril formation / Crosslinking of collagen fibrils / collagen biosynthetic process / Collagen chain trimerization / negative regulation of monocyte activation ...cellular response to fluoride / collagen type I trimer / tooth mineralization / cellular response to vitamin E / collagen type IV trimer / Anchoring fibril formation / Crosslinking of collagen fibrils / collagen biosynthetic process / Collagen chain trimerization / negative regulation of monocyte activation / Defective VWF binding to collagen type I / platelet-derived growth factor binding / bone trabecula formation / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / calcium-independent cell-matrix adhesion / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / negative regulation of transforming growth factor beta production / Fibronectin matrix formation / intramembranous ossification / embryonic skeletal system development / Extracellular matrix organization / positive regulation of substrate-dependent cell migration, cell attachment to substrate / cartilage development involved in endochondral bone morphogenesis / extracellular matrix structural constituent conferring tensile strength / Collagen biosynthesis and modifying enzymes / neural crest cell migration involved in autonomic nervous system development / peptidase activator activity / skin morphogenesis / fibrinogen complex / collagen-activated tyrosine kinase receptor signaling pathway / peptide cross-linking / endochondral ossification / Platelet Adhesion to exposed collagen / integrin activation / ALK mutants bind TKIs / cell-substrate junction assembly / cellular response to fibroblast growth factor stimulus / collagen fibril organization / negative regulation of cell-substrate adhesion / response to steroid hormone / face morphogenesis / biological process involved in interaction with symbiont / proteoglycan binding / Molecules associated with elastic fibres / Scavenging by Class A Receptors / skin development / Assembly of collagen fibrils and other multimeric structures / MET activates PTK2 signaling / extracellular matrix structural constituent / Syndecan interactions / GP1b-IX-V activation signalling / p130Cas linkage to MAPK signaling for integrins / blood vessel development / endodermal cell differentiation / RUNX2 regulates osteoblast differentiation / Platelet Aggregation (Plug Formation) / GRB2:SOS provides linkage to MAPK signaling for Integrins / Collagen degradation / endoplasmic reticulum-Golgi intermediate compartment / protein localization to nucleus / Non-integrin membrane-ECM interactions / basement membrane / ECM proteoglycans / response to hyperoxia / Integrin cell surface interactions / positive regulation of axon extension / positive regulation of epithelial to mesenchymal transition / response to mechanical stimulus / cellular response to retinoic acid / cellular response to epidermal growth factor stimulus / GPVI-mediated activation cascade / cellular response to transforming growth factor beta stimulus / response to cAMP / collagen binding / visual perception / Degradation of the extracellular matrix / Integrin signaling / ossification / extracellular matrix organization / substrate adhesion-dependent cell spreading / regulation of ERK1 and ERK2 cascade / cell-matrix adhesion / extracellular matrix / platelet alpha granule lumen / secretory granule / skeletal system development / acute-phase response / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / cellular response to glucose stimulus / sensory perception of sound / cellular response to amino acid stimulus / Post-translational protein phosphorylation / regulation of protein phosphorylation / Signaling by high-kinase activity BRAF mutants / wound healing / MAP2K and MAPK activation / response to insulin Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Sladek, B. / Campbell, I.D. / Vakonakis, I. | ||||||
![]() | ![]() Title: Structural analysis of collagen type I interactions with human fibronectin reveals a cooperative binding mode Authors: Erat, M.C. / Sladek, B. / Campbell, I.D. / Vakonakis, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.5 KB | Display | ![]() |
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PDB format | ![]() | 78.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 479.8 KB | Display | ![]() |
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Full document | ![]() | 481.2 KB | Display | |
Data in XML | ![]() | 10.8 KB | Display | |
Data in CIF | ![]() | 13.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ejhS S: Starting model for refinement |
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Similar structure data |
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Links
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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
-Collagen alpha-1(I) ... , 2 types, 2 molecules FE
#2: Protein/peptide | Mass: 2280.543 Da / Num. of mol.: 1 / Fragment: ColI.260, UNP residues 254-275 / Source method: obtained synthetically / Details: Standard peptide synthesis / References: UniProt: P02452 |
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#3: Protein/peptide | Mass: 2280.543 Da / Num. of mol.: 1 / Fragment: ColI.260, UNP residues 254-275 / Source method: obtained synthetically / Details: Standard peptide synthesis / References: UniProt: P02452 |
-Protein / Sugars , 2 types, 4 molecules BA![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 10891.985 Da / Num. of mol.: 2 / Fragment: 8-9FnI, UNP residues 516-608 / Mutation: N528Q, R534K Source method: isolated from a genetically manipulated source Details: Gene fragment integrated in the AOX1 locus / Source: (gene. exp.) ![]() ![]() #4: Sugar | |
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-Non-polymers , 2 types, 45 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-GOL / |
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#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.05 % / Mosaicity: 0.841 ° |
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Crystal grow | Temperature: 293.1 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES pH 7.5, 4.3M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 293.1K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2009 / Details: cylindrical grazing incidence mirror |
Radiation | Monochromator: silicon monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.558→46.676 Å / Num. all: 16850 / Num. obs: 16804 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 2.4 / Num. measured all: 8589 / Num. unique all: 2462 / Rsym value: 0.442 / % possible all: 100 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Rfactor: 39.27 / Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB Entry 3EJH, Chain A and part of chain E Resolution: 2.6→46.648 Å / Occupancy max: 1 / Occupancy min: 0.43 / FOM work R set: 0.798 / SU ML: 0.99 / Isotropic thermal model: TLS / σ(F): 0.19 / Stereochemistry target values: ML Details: The SF file contains Friedel pairs under I/F_plus and I/F_minus column.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.82 Å2 / ksol: 0.381 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 176.72 Å2 / Biso mean: 57.63 Å2 / Biso min: 19.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→46.648 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: 9
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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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