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- PDB-6mfa: Fragment of human fibronectin containing the 4th-7th type III domains -

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Basic information

Entry
Database: PDB / ID: 6mfa
TitleFragment of human fibronectin containing the 4th-7th type III domains
ComponentsFibronectin
KeywordsCELL ADHESION / FN3 DOMAIN / FIBRONECTIN
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 / proteoglycan binding / Molecules associated with elastic fibres / extracellular matrix structural constituent / MET activates PTK2 signaling / 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 / regulation of ERK1 and ERK2 cascade / cell-matrix adhesion / substrate adhesion-dependent cell spreading / extracellular matrix / platelet alpha granule lumen / acute-phase response / integrin-mediated signaling pathway / Post-translational protein phosphorylation / Cell surface interactions at the vascular wall / wound healing / Signaling by high-kinase activity BRAF mutants / regulation of protein phosphorylation / 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) / 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 / GPER1 signaling / positive regulation of fibroblast proliferation / Signaling by BRAF and RAF1 fusions / Signaling by ALK fusions and activated point mutants / integrin binding / Platelet degranulation / heart development / heparin binding / nervous system development / regulation of cell shape / Interleukin-4 and Interleukin-13 signaling / protease binding / angiogenesis / collagen-containing extracellular matrix / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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
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 / EGF-like domain signature 1. / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.754 Å
AuthorsLoa, S. / Mou, T.C. / Sprang, S.R. / Briknarova, K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)P20GM103546 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM114657 United States
CitationJournal: To Be Published
Title: Fragment of human fibronectin containing the 4th-7th type III domains, crystal form I
Authors: Mou, T.C. / Loa, S. / Sprang, S.R. / Briknarova, K.
History
DepositionSep 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)40,0381
Polymers40,0381
Non-polymers00
Water6,990388
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)139.811, 40.561, 59.217
Angle α, β, γ (deg.)90.00, 98.27, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1553-

HOH

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Components

#1: Protein Fibronectin / FN / Cold-insoluble globulin / CIG


Mass: 40037.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FN1, FN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02751
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.08 Å3/Da / Density % sol: 40.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M MES pH 5.5, 7% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Apr 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.75→33.045 Å / Num. obs: 31639 / % possible obs: 95.03 % / Redundancy: 2.9 % / Biso Wilson estimate: 17.41 Å2 / Rrim(I) all: 0.1 / Net I/σ(I): 9.5
Reflection shellResolution: 1.75→1.82 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2939 / Rrim(I) all: 0.66 / % possible all: 89.19

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DFT

5dft


Resolution: 1.754→33.045 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2384 1998 6.32 %
Rwork0.1908 --
obs0.1937 31625 95.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.754→33.045 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2784 0 0 388 3172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022896
X-RAY DIFFRACTIONf_angle_d0.5813994
X-RAY DIFFRACTIONf_dihedral_angle_d8.532420
X-RAY DIFFRACTIONf_chiral_restr0.047478
X-RAY DIFFRACTIONf_plane_restr0.004523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7541-1.79790.33231300.29851928X-RAY DIFFRACTION88
1.7979-1.84660.33131380.29122034X-RAY DIFFRACTION91
1.8466-1.90090.2831310.26461964X-RAY DIFFRACTION90
1.9009-1.96220.30371420.24242095X-RAY DIFFRACTION95
1.9622-2.03240.30671440.21822129X-RAY DIFFRACTION96
2.0324-2.11370.24581410.20622104X-RAY DIFFRACTION95
2.1137-2.20990.22621420.19822109X-RAY DIFFRACTION96
2.2099-2.32640.26091430.20192124X-RAY DIFFRACTION96
2.3264-2.47210.27271420.20792099X-RAY DIFFRACTION95
2.4721-2.66290.27171460.21032179X-RAY DIFFRACTION97
2.6629-2.93070.2421480.20162187X-RAY DIFFRACTION98
2.9307-3.35440.22761480.17552188X-RAY DIFFRACTION98
3.3544-4.22490.2191490.14662213X-RAY DIFFRACTION98
4.2249-33.05070.16381540.15092274X-RAY DIFFRACTION98

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