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- PDB-6xay: Structure of a fragment of human fibronectin containing the 10th,... -

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Basic information

Entry
Database: PDB / ID: 6xay
TitleStructure of a fragment of human fibronectin containing the 10th, 11th and 12th type III domains
ComponentsFibronectin
KeywordsCELL ADHESION / Fibronectin / FN3
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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsMou, T.C. / Nepomuceno, P.A. / Sprang, S.R. / Briknarova, K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH P20 GM103546 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH 5R01 GM114657 United States
CitationJournal: To Be Published
Title: Fragment of human fibronectin containing the 10th, 11th and 12th type III domains
Authors: Mou, T.C. / Nepomuceno, P.A. / Sprang, S.R. / Briknarova, K.
History
DepositionJun 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.pH / _exptl_crystal_grow.pdbx_details
Revision 1.2Oct 13, 2021Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fibronectin
B: Fibronectin
C: Fibronectin
D: Fibronectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,84610
Polymers119,2944
Non-polymers5536
Water2,468137
1
A: Fibronectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0083
Polymers29,8231
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fibronectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1004
Polymers29,8231
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fibronectin


Theoretical massNumber of molelcules
Total (without water)29,8231
Polymers29,8231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Fibronectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9162
Polymers29,8231
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.085, 440.367, 60.474
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3

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Components

#1: Protein
Fibronectin / FN / Cold-insoluble globulin / CIG


Mass: 29823.416 Da / Num. of mol.: 4 / Mutation: V1643G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FN1, FN / Production host: Escherichia coli (E. coli) / References: UniProt: P02751
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.49 Å3/Da / Density % sol: 64.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.5M (NH4)2SO4, 0.1M Citric acid pH 4.0, 30%(v/v)PEG 600, 10%(v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.48→37.4 Å / Num. obs: 55470 / % possible obs: 92.11 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rpim(I) all: 0.033 / Rrim(I) all: 0.097 / Net I/σ(I): 12.3
Reflection shellResolution: 2.48→2.57 Å / Mean I/σ(I) obs: 2.9 / Num. unique obs: 20331 / CC1/2: 0.732 / Rpim(I) all: 0.2342 / Rrim(I) all: 0.5042

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Processing

Software
NameVersionClassification
PHENIX1.16refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DFT

5dft


Resolution: 2.48→37.4 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.296 1998 -
Rwork0.246 --
obs-55470 92.1 %
Displacement parametersBiso mean: 72.06 Å2
Refinement stepCycle: LAST / Resolution: 2.48→37.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8142 0 36 137 8315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058351
X-RAY DIFFRACTIONf_angle_d0.74611456
X-RAY DIFFRACTIONf_dihedral_angle_d20.8563085
X-RAY DIFFRACTIONf_chiral_restr0.0531400
X-RAY DIFFRACTIONf_plane_restr0.0061454
LS refinement shellResolution: 2.48→2.57 Å
RfactorNum. reflection% reflection
Rfree0.3811 0 -
Rwork0.3534 0 -
obs--84 %
Refinement TLS params.Method: refined / Origin x: -31.5598 Å / Origin y: -54.8236 Å / Origin z: -0.079 Å
111213212223313233
T-0.079 Å20.154 Å21.2072 Å2-0.2824 Å2-0.0609 Å2--0.1004 Å2
L-0.3494 °20.1585 °20.2732 °2-2.8475 °2-0.0664 °2---0.4175 °2
S0.5641 Å °0.0749 Å °-0.4936 Å °-1.2258 Å °-0.2284 Å °0.2293 Å °0.6097 Å °0.0537 Å °0.1992 Å °
Refinement TLS groupSelection details: all

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