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- PDB-2rky: Crystal structure of the fourth and fifth fibronectin F1 modules ... -

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Basic information

Entry
Database: PDB / ID: 2rky
TitleCrystal structure of the fourth and fifth fibronectin F1 modules in complex with a fragment of staphylococcus aureus fnbpa-1
Components
  • Fibronectin
  • Fibronectin-binding protein
KeywordsCELL ADHESION / Fibronectin / 4F15F1 / Beta zipper / Staphylococcus aureus / Acute phase / Alternative splicing / Extracellular matrix / Glycoprotein / Heparin-binding / Phosphorylation / Pyrrolidone carboxylic acid / Secreted / Sulfation / Cell wall / Peptidoglycan-anchor / Virulence
Function / homology
Function and homology information


aggregation of unicellular organisms / 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 ...aggregation of unicellular organisms / 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 / fibrinogen binding / 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 / fibronectin binding / 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 binding repeat / Fibronectin binding repeat / Fibrinogen-binding domain 2 / C-terminus of bacterial fibrinogen-binding adhesin / SDR-like Ig domain / Bacterial Ig domain / Fibrogen-binding domain 1 / Fibronectin type I domain / : ...: / Fibronectin binding repeat / Fibronectin binding repeat / Fibrinogen-binding domain 2 / C-terminus of bacterial fibrinogen-binding adhesin / SDR-like Ig domain / Bacterial Ig domain / Fibrogen-binding domain 1 / Fibronectin type I domain / : / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Complement Module, domain 1 / Complement Module; domain 1 / 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 / Adhesion domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor 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 / Ribbon / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
: / THIOCYANATE ION / Fibronectin / Fibronectin-binding protein A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsBingham, R.J.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Crystal structures of fibronectin-binding sites from Staphylococcus aureus FnBPA in complex with fibronectin domains
Authors: Bingham, R.J. / Meenan, N.A. / Schwarz-Linek, U. / Turkenburg, J.P. / Garman, E.F. / Potts, J.R.
History
DepositionOct 18, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fibronectin
C: Fibronectin
B: Fibronectin-binding protein
D: Fibronectin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,91310
Polymers26,5834
Non-polymers3306
Water4,216234
1
A: Fibronectin
D: Fibronectin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4084
Polymers13,2922
Non-polymers1162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-9.9 kcal/mol
Surface area6620 Å2
MethodPISA
2
C: Fibronectin
B: Fibronectin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5056
Polymers13,2922
Non-polymers2134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-9.2 kcal/mol
Surface area6950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.596, 36.244, 73.551
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-251-

HOH

21A-255-

HOH

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Components

#1: Protein Fibronectin / Human fibronectin module pair 4F1-5F1


Mass: 10534.699 Da / Num. of mol.: 2 / Fragment: UNP residues 183-275
Source method: isolated from a genetically manipulated source
Details: human / Source: (gene. exp.) Homo sapiens (human) / Gene: FN1 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: P02751
#2: Protein/peptide Fibronectin-binding protein / Staphylococcus aureus fibronectin binding protein / FNBP


Mass: 2757.012 Da / Num. of mol.: 2 / Fragment: UNP residues 508-530 / Source method: obtained synthetically / Details: Peptide synthesis / References: UniProt: P14738
#3: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.22 Å3/Da / Density % sol: 44.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100mM Tris-HCl, pH8.5, 0.15M Potassium thiocyanate, 20% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 9, 2007
RadiationMonochromator: Daimond (111), Ge (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.8→30.51 Å / Num. all: 21474 / Num. obs: 21474 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3.7 / Redundancy: 7.1 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Χ2: 1.858 / Net I/σ(I): 29
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 6.3 / Num. unique all: 1630 / Rsym value: 0.488 / Χ2: 2.048 / % possible all: 98.97

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3data extraction
RefinementStarting model: Previous lower resolution structure

Resolution: 1.8→30.51 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.435 / SU ML: 0.078 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3.7 / ESU R: 0.129 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1142 5 %RANDOM
Rwork0.181 ---
all0.183 22616 --
obs0.183 21474 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.819 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1775 0 16 234 2025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211827
X-RAY DIFFRACTIONr_angle_refined_deg1.381.922454
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2365224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50724.14994
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64615325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5021516
X-RAY DIFFRACTIONr_chiral_restr0.0050.02246
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021394
X-RAY DIFFRACTIONr_nbd_refined0.2290.2278
X-RAY DIFFRACTIONr_nbtor_refined0.2980.2483
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.285
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3110.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.28
X-RAY DIFFRACTIONr_mcbond_it2.42621108
X-RAY DIFFRACTIONr_mcangle_it3.67331763
X-RAY DIFFRACTIONr_scbond_it3.1532719
X-RAY DIFFRACTIONr_scangle_it4.5243689
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 86 -
Rwork0.22 1544 -
all-1630 -
obs-1630 98.97 %

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