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- PDB-1fna: CRYSTAL STRUCTURE OF THE TENTH TYPE III CELL ADHESION MODULE OF H... -

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Basic information

Entry
Database: PDB / ID: 1fna
TitleCRYSTAL STRUCTURE OF THE TENTH TYPE III CELL ADHESION MODULE OF HUMAN FIBRONECTIN
ComponentsFIBRONECTIN CELL-ADHESION MODULE TYPE III-10
KeywordsCELL ADHESION PROTEIN
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 / MET activates PTK2 signaling / extracellular matrix structural constituent / 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 / substrate adhesion-dependent cell spreading / regulation of ERK1 and ERK2 cascade / cell-matrix adhesion / extracellular matrix / platelet alpha granule lumen / acute-phase response / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / Post-translational protein phosphorylation / regulation of protein phosphorylation / Signaling by high-kinase activity BRAF mutants / wound healing / MAP2K and MAPK activation / response to wounding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / GPER1 signaling / Signaling downstream of RAS mutants / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Signaling by BRAF and RAF1 fusions / positive regulation of fibroblast proliferation / Signaling by ALK fusions and activated point mutants / integrin binding / Platelet degranulation / nervous system development / heparin binding / heart development / regulation of cell shape / angiogenesis / Interleukin-4 and Interleukin-13 signaling / collagen-containing extracellular matrix / protease binding / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / blood microparticle / 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-II collagen-binding domain profile. ...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 / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsDickinson, C.D. / Veerapandian, B. / Ely, K.R.
CitationJournal: J.Mol.Biol. / Year: 1994
Title: Crystal structure of the tenth type III cell adhesion module of human fibronectin.
Authors: Dickinson, C.D. / Veerapandian, B. / Dai, X.P. / Hamlin, R.C. / Xuong, N.H. / Ruoslahti, E. / Ely, K.R.
History
DepositionJan 11, 1994Processing site: BNL
Revision 1.0Apr 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_sheet.number_strands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FIBRONECTIN CELL-ADHESION MODULE TYPE III-10


Theoretical massNumber of molelcules
Total (without water)9,6921
Polymers9,6921
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.700, 35.100, 37.700
Angle α, β, γ (deg.)90.00, 107.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FIBRONECTIN CELL-ADHESION MODULE TYPE III-10


Mass: 9691.788 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P02751

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.58 %
Crystal grow
*PLUS
pH: 8.6 / Method: unknown
Components of the solutions
*PLUS
IDCommon nameCrystal-IDSol-ID
1Tris-maleate1reservoir
2PEG45001reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.75 Å / Num. obs: 7250 / % possible obs: 96 % / Num. measured all: 34949 / Rmerge(I) obs: 0.072

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.8→10 Å / Rfactor obs: 0.18
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms826 0 0 0 826
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / Num. reflection obs: 6996 / Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d0.042
X-RAY DIFFRACTIONp_planar_d0.037
X-RAY DIFFRACTIONp_plane_restr0.016

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