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- PDB-3r8q: Structure of Fibronectin domain 12-14 -

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Basic information

Entry
Database: PDB / ID: 3r8q
TitleStructure of Fibronectin domain 12-14
ComponentsFibronectin
KeywordsCELL ADHESION / Fibronectin / heparin / FNIII / heparin binding
Function / homology
Function and homology information


negative regulation of monocyte activation / negative regulation of transforming growth factor beta production / Extracellular matrix organization / positive regulation of substrate-dependent cell migration, cell attachment to substrate / Fibronectin matrix formation / calcium-independent cell-matrix adhesion / neural crest cell migration involved in autonomic nervous system development / peptidase activator activity / fibrinogen complex / peptide cross-linking ...negative regulation of monocyte activation / negative regulation of transforming growth factor beta production / Extracellular matrix organization / positive regulation of substrate-dependent cell migration, cell attachment to substrate / Fibronectin matrix formation / calcium-independent cell-matrix adhesion / 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 / proteoglycan binding / biological process involved in interaction with symbiont / extracellular matrix structural constituent / Molecules associated with elastic fibres / MET activates PTK2 signaling / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / response to muscle activity / endoplasmic reticulum-Golgi intermediate compartment / endodermal cell differentiation / GRB2:SOS provides linkage to MAPK signaling for Integrins / regulation of protein phosphorylation / basement membrane / Non-integrin membrane-ECM interactions / ECM proteoglycans / Integrin cell surface interactions / positive regulation of axon extension / endothelial cell migration / regulation of ERK1 and ERK2 cascade / collagen binding / Degradation of the extracellular matrix / Integrin signaling / extracellular matrix / substrate adhesion-dependent cell spreading / platelet alpha granule lumen / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cell-matrix adhesion / acute-phase response / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / Post-translational protein phosphorylation / wound healing / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / response to wounding / positive regulation of fibroblast proliferation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / 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 / Signaling by BRAF and RAF1 fusions / Signaling by ALK fusions and activated point mutants / integrin binding / GPER1 signaling / Platelet degranulation / nervous system development / heparin binding / regulation of cell shape / heart development / protease binding / : / Interleukin-4 and Interleukin-13 signaling / angiogenesis / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / apical plasma membrane / receptor ligand activity / 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
Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / : / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. ...Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / : / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Kringle-like fold / Fibronectin type III domain / EGF-like domain signature 1. / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsZaccai, N.R. / Agnew, C. / Brady, R.L.
CitationJournal: To be Published
Title: Structure of Fibronectin domain 12-14
Authors: Zaccai, N.R. / Agnew, C. / Brady, R.L.
History
DepositionMar 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fibronectin


Theoretical massNumber of molelcules
Total (without water)31,7721
Polymers31,7721
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.010, 36.890, 75.970
Angle α, β, γ (deg.)90.000, 94.570, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fibronectin / FN / Cold-insoluble globulin / CIG / Anastellin / Ugl-Y1 / Ugl-Y2 / Ugl-Y3


Mass: 31772.100 Da / Num. of mol.: 1 / Fragment: unp residues 1722-1992
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Fibronectin 1, FN, FN1 / Plasmid: popinF / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta plyS / References: UniProt: P02751
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Na HEPES, 0.8 M sodium dihydrogen phosphate, 0.8 M potassium dihydrogen phosphate, supplemented with 35% glycerol for cryo-protection, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionRedundancy: 6.4 % / Av σ(I) over netI: 8.1 / Number: 68821 / Rsym value: 0.076 / D res high: 2.4 Å / D res low: 75.728 Å / Num. obs: 10754 / % possible obs: 93.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
7.5944.4699.110.0550.0556.2
5.377.5999.510.0650.0656.6
4.385.3799.710.0530.0537
3.794.3899.910.0540.0547.1
3.393.7910010.0640.0647.2
3.13.3999.910.0790.0797.3
2.873.110010.1190.1197.3
2.682.8798.710.160.166.4
2.532.6887.510.2030.2034.8
2.42.5367.910.2580.2584.3
ReflectionResolution: 2.4→75.728 Å / Num. all: 10754 / Num. obs: 10754 / % possible obs: 93.3 % / Redundancy: 6.4 % / Rsym value: 0.076 / Net I/σ(I): 17.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.4-2.534.30.2583480711170.25867.9
2.53-2.684.80.2033.7654813660.20387.5
2.68-2.876.40.164.7943814650.1698.7
2.87-3.17.30.1196.11005613830.119100
3.1-3.397.30.0798.9930112790.07999.9
3.39-3.797.20.06410.2829011520.064100
3.79-4.387.10.05411.5728010270.05499.9
4.38-5.3770.05311.462008890.05399.7
5.37-7.596.60.0658.644716810.06599.5
7.59-44.4636.20.0551024303950.05599.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASERphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→44.463 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8272 / SU ML: 0.33 / σ(F): 0 / Phase error: 23.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2362 526 4.89 %RANDOM
Rwork0.1839 ---
obs0.1863 10746 93.1 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.376 Å2 / ksol: 0.377 e/Å3
Displacement parametersBiso max: 82.38 Å2 / Biso mean: 26.178 Å2 / Biso min: 9.47 Å2
Baniso -1Baniso -2Baniso -3
1--2.4793 Å2-0 Å23.8602 Å2
2--2.0633 Å2-0 Å2
3---0.416 Å2
Refinement stepCycle: LAST / Resolution: 2.4→44.463 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2086 0 0 123 2209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082133
X-RAY DIFFRACTIONf_angle_d1.1862926
X-RAY DIFFRACTIONf_chiral_restr0.066355
X-RAY DIFFRACTIONf_plane_restr0.005374
X-RAY DIFFRACTIONf_dihedral_angle_d15.097809
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.64150.30971090.22552021213075
2.6415-3.02370.2991510.21192658280998
3.0237-3.80920.23481140.177627482862100
3.8092-44.47060.19381520.16632793294599

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