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- PDB-3t1w: Structure of the four-domain fragment Fn7B89 of oncofetal fibronectin -

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Basic information

Entry
Database: PDB / ID: 3t1w
TitleStructure of the four-domain fragment Fn7B89 of oncofetal fibronectin
Componentsfour-domain fibronectin fragment
KeywordsPROTEIN BINDING / human fibronectin / Fn type-III domain / oncofetal splice variant / extra-domain B / EIIIB / ED-B / angiogenesis / integrin / fibronectin / extracellular matrix
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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fibronectin / Fibronectin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSchiefner, A. / Skerra, A.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Extra-domain B in oncofetal fibronectin structurally promotes fibrillar head-to-tail dimerization of extracellular matrix protein.
Authors: Schiefner, A. / Gebauer, M. / Skerra, A.
History
DepositionJul 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
Revision 1.2Jun 26, 2013Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 13, 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 / 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

Downloads & links

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Assembly

Deposited unit
A: four-domain fibronectin fragment


Theoretical massNumber of molelcules
Total (without water)40,9671
Polymers40,9671
Non-polymers00
Water2,126118
1
A: four-domain fibronectin fragment

A: four-domain fibronectin fragment


Theoretical massNumber of molelcules
Total (without water)81,9342
Polymers81,9342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3700 Å2
ΔGint-7 kcal/mol
Surface area37660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)211.980, 29.115, 82.241
Angle α, β, γ (deg.)90.00, 111.42, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein four-domain fibronectin fragment


Mass: 40967.176 Da / Num. of mol.: 1 / Fragment: unp residues 920-1286
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DKFZp686O12165, NP_997647 / Plasmid: pASK75-Fn7B89-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6MZM7, UniProt: P02751*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.88 Å3/Da / Density % sol: 57.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 26 %(w/v) PEG3350, 0.1 M Tris-HCl, 0.2 M NaCl, 5 %(v/v) Isopropanol, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2009 / Details: double crystal
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 19034 / Num. obs: 18943 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 44.1 Å2 / Rsym value: 0.056 / Net I/σ(I): 18.8
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 2147 / Rsym value: 0.425 / % possible all: 99.7

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FNF

1fnf


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.887 / SU B: 18.676 / SU ML: 0.198 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27693 976 5.2 %RANDOM
Rwork0.22755 ---
obs0.23008 17966 99.76 %-
all-17966 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.608 Å2
Baniso -1Baniso -2Baniso -3
1--1.98 Å20 Å2-0.41 Å2
2--2.18 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2821 0 0 118 2939
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222890
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.151.9663975
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2975367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.46624.508122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.0415433
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4461517
X-RAY DIFFRACTIONr_chiral_restr0.0690.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0222216
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4191.51848
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.8282.53056
X-RAY DIFFRACTIONr_scbond_it1.6283.51042
X-RAY DIFFRACTIONr_scangle_it2.93510919
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 72 -
Rwork0.29 1299 -
obs--99.85 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.1940.58152.33062.76190.240311.67810.1716-0.84540.2132-0.01670.0506-0.3002-0.24360.7075-0.22230.326-0.10750.06760.5063-0.03350.269553.06698.557835.2632
224.511-3.08495.71380.4068-0.73521.3983-0.4224-1.3156-0.55120.11830.35980.0443-0.2928-0.31920.06260.58840.2451-0.12121.08670.1870.56133.00560.420412.399
34.073-0.00091.3012.19010.30763.98890.0110.25780.0211-0.2066-0.0293-0.17970.03110.29270.01830.17510.0090.02270.03850.01410.1741-46.641814.7677-5.7583
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1173 - 1264
2X-RAY DIFFRACTION2A1265 - 1446
3X-RAY DIFFRACTION3A1447 - 1540

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