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- PDB-2gee: Crystal Structure of Human Type III Fibronectin Extradomain B and... -

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Basic information

Entry
Database: PDB / ID: 2gee
TitleCrystal Structure of Human Type III Fibronectin Extradomain B and Domain 8
Componentshypothetical protein
KeywordsPROTEIN BINDING / ONCOPROTEIN / fibronectin / EIIIB / cancer / neovascularization / cell adhesion
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 / endoplasmic reticulum-Golgi intermediate compartment / GRB2:SOS provides linkage to MAPK signaling for Integrins / 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 / extracellular matrix / substrate adhesion-dependent cell spreading / regulation of ERK1 and ERK2 cascade / cell-matrix adhesion / platelet alpha granule lumen / acute-phase response / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / Post-translational protein phosphorylation / wound healing / regulation of protein phosphorylation / Signaling by high-kinase activity BRAF mutants / 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 / positive regulation of fibroblast proliferation / GPER1 signaling / Signaling by BRAF and RAF1 fusions / Signaling by ALK fusions and activated point mutants / integrin binding / Platelet degranulation / heparin binding / heart development / nervous system development / regulation of cell shape / protease binding / Interleukin-4 and Interleukin-13 signaling / 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 / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsBencharit, S. / Cui, C.B. / Siddiqui, A. / Howard-Williams, E.L. / Aukhil, I.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural insights into fibronectin type III domain-mediated signaling.
Authors: Bencharit, S. / Cui, C.B. / Siddiqui, A. / Howard-Williams, E.L. / Sondek, J. / Zuobi-Hasona, K. / Aukhil, I.
History
DepositionMar 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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

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Assembly

Deposited unit
A: hypothetical protein


Theoretical massNumber of molelcules
Total (without water)22,0971
Polymers22,0971
Non-polymers00
Water6,918384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.407, 55.288, 74.903
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein hypothetical protein


Mass: 22097.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DKFZp686O1166 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: Q6MZU5, UniProt: P02751*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.19 Å3/Da / Density % sol: 39.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10% (w/v) PEG-3350 and 0.2 mM ammonium citrate. , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 9, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→28.36 Å / Num. obs: 12553 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 15.9 Å2 / Rsym value: 0.082
Reflection shellResolution: 2.01→2.13 Å / % possible all: 98.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: fragment of Repeat domain 8 from 1fnf

1fnf


Resolution: 2.01→28.36 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1284205.73 / Data cutoff high rms absF: 1284205.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.301 1291 10.3 %RANDOM
Rwork0.249 ---
all0.249 12553 --
obs0.249 12512 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 79.1065 Å2 / ksol: 0.364699 e/Å3
Displacement parametersBiso mean: 39.7 Å2
Baniso -1Baniso -2Baniso -3
1-13.43 Å20 Å20 Å2
2---10.62 Å20 Å2
3----2.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.01→28.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1443 0 0 384 1827
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d26.9
X-RAY DIFFRACTIONc_improper_angle_d1.21
X-RAY DIFFRACTIONc_mcbond_it1.741.5
X-RAY DIFFRACTIONc_mcangle_it2.732
X-RAY DIFFRACTIONc_scbond_it2.422
X-RAY DIFFRACTIONc_scangle_it3.442.5
LS refinement shellResolution: 2.01→2.13 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.353 206 10.2 %
Rwork0.318 1806 -
obs--98.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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