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- PDB-2cg7: SECOND AND THIRD FIBRONECTIN TYPE I MODULE PAIR (CRYSTAL FORM II). -

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Basic information

Entry
Database: PDB / ID: 2cg7
TitleSECOND AND THIRD FIBRONECTIN TYPE I MODULE PAIR (CRYSTAL FORM II).
ComponentsFIBRONECTIN
KeywordsSIGNALING PROTEIN / FIBRONECTIN / 2F13F1 / ACUTE PHASE / ALTERNATIVE SPLICING / CELL ADHESION / GLYCOPROTEIN / HEPARIN-BINDING / PHOSPHORYLATION / PYRROLIDONE CARBOXYLIC ACID / SULFATION
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 / : / Complement Module, domain 1 / Complement Module; domain 1 / Fibronectin type II domain / Fibronectin type II domain superfamily ...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 / 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 / Ribbon / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsRudino-Pinera, E. / Ravelli, R.B.G. / Sheldrick, G.M. / Nanao, M.H. / Werner, J.M. / Schwarz-Linek, U. / Potts, J.R. / Garman, E.F.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: The Solution and Crystal Structures of a Module Pair from the Staphylococcus Aureus-Binding Site of Human Fibronectin-A Tale with a Twist.
Authors: Rudino-Pinera, E. / Ravelli, R.B.G. / Sheldrick, G.M. / Nanao, M.H. / Korostelev, V.V. / Werner, J.M. / Schwarz-Linek, U. / Potts, J.R. / Garman, E.F.
History
DepositionFeb 27, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)10,1201
Polymers10,1201
Non-polymers00
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)52.651, 29.419, 51.009
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2138-

HOH

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Components

#1: Protein FIBRONECTIN / FN / COLD-INSOLUBLE GLOBULIN / CIG


Mass: 10120.389 Da / Num. of mol.: 1 / Fragment: RESIDUES 93-182 (62-151 IN COORDINATES)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: PICHIA PASTORIS (fungus) / References: UniProt: P02751
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFIBRONECTINS BIND CELL SURFACES AND VARIOUS COMPOUNDS INCLUDING COLLAGEN, FIBRIN, HEPARIN, DNA, AND ACTIN
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 Å3/Da / Density % sol: 38.4 %
Crystal growpH: 7 / Details: WATER AND 0.02% SODIUM AZIDE, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 18, 2006 / Details: FIXED RADII TOROIDAL MIRROR
RadiationMonochromator: GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.2→29.44 Å / Num. obs: 167693 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 8.44 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 6.6
Reflection shellResolution: 1.2→1.26 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.1 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CG6

2cg6


Resolution: 1.2→52.63 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.834 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1258 5.1 %RANDOM
Rwork0.189 ---
obs0.19 23388 96.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.38 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å20 Å20 Å2
2---0.02 Å20 Å2
3----1.17 Å2
Refinement stepCycle: LAST / Resolution: 1.2→52.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms703 0 0 155 858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.021914
X-RAY DIFFRACTIONr_bond_other_d0.0020.02787
X-RAY DIFFRACTIONr_angle_refined_deg1.3121.9461254
X-RAY DIFFRACTIONr_angle_other_deg0.89131850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7345124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.49622.32643
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.95615168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8031511
X-RAY DIFFRACTIONr_chiral_restr0.130.2121
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021108
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02208
X-RAY DIFFRACTIONr_nbd_refined0.1720.2171
X-RAY DIFFRACTIONr_nbd_other0.2070.2856
X-RAY DIFFRACTIONr_nbtor_refined0.1710.2427
X-RAY DIFFRACTIONr_nbtor_other0.0820.2541
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.295
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1970.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.238
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0411.5728
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2912916
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7163425
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2054.5338
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.2→1.23 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.286 81
Rwork0.252 1696

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