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- PDB-5dft: Structure of the Eleventh Type III Domain from Human Fibronectin -

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Basic information

Entry
Database: PDB / ID: 5dft
TitleStructure of the Eleventh Type III Domain from Human Fibronectin
ComponentsFibronectin
KeywordsCELL ADHESION / FN3 domain / fibronectin
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 / Molecules associated with elastic fibres / proteoglycan binding / 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 / Non-integrin membrane-ECM interactions / basement membrane / endoplasmic reticulum-Golgi intermediate compartment / ECM proteoglycans / positive regulation of axon extension / Integrin cell surface interactions / collagen binding / Degradation of the extracellular matrix / Integrin signaling / substrate adhesion-dependent cell spreading / cell-matrix adhesion / extracellular matrix / regulation of ERK1 and ERK2 cascade / 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 / Signaling by ALK fusions and activated point mutants / response to wounding / GPER1 signaling / 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 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of fibroblast proliferation / Signaling by BRAF and RAF1 fusions / integrin binding / Platelet degranulation / heparin binding / nervous system development / heart development / regulation of cell shape / Interleukin-4 and Interleukin-13 signaling / angiogenesis / collagen-containing extracellular matrix / protease binding / 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-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 / 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
CITRIC ACID / Fibronectin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsRusnac, D.-V. / Mou, T.C. / Sprang, S.R. / Briknarova, K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103546 United States
National Science Foundation (NSF, United States)MCB-0846132 United States
CitationJournal: To Be Published
Title: Structure of the Eleventh Type III Domain from Human Fibronectin
Authors: Rusnac, D.-V. / Mou, T.C. / Sprang, S.R. / Briknarova, K.
History
DepositionAug 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fibronectin
B: Fibronectin
C: Fibronectin
D: Fibronectin
E: Fibronectin
F: Fibronectin
G: Fibronectin
H: Fibronectin
I: Fibronectin
J: Fibronectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,97211
Polymers107,78010
Non-polymers1921
Water2,342130
1
A: Fibronectin


Theoretical massNumber of molelcules
Total (without water)10,7781
Polymers10,7781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fibronectin


Theoretical massNumber of molelcules
Total (without water)10,7781
Polymers10,7781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fibronectin


Theoretical massNumber of molelcules
Total (without water)10,7781
Polymers10,7781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Fibronectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9702
Polymers10,7781
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Fibronectin


Theoretical massNumber of molelcules
Total (without water)10,7781
Polymers10,7781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Fibronectin


Theoretical massNumber of molelcules
Total (without water)10,7781
Polymers10,7781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Fibronectin


Theoretical massNumber of molelcules
Total (without water)10,7781
Polymers10,7781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Fibronectin


Theoretical massNumber of molelcules
Total (without water)10,7781
Polymers10,7781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Fibronectin


Theoretical massNumber of molelcules
Total (without water)10,7781
Polymers10,7781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Fibronectin


Theoretical massNumber of molelcules
Total (without water)10,7781
Polymers10,7781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.493, 107.402, 210.337
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-205-

HOH

21C-204-

HOH

31E-205-

HOH

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Components

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


Mass: 10777.957 Da / Num. of mol.: 10
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-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.1M sodium citrate, 0.1M citric acid and 0.1M sodium iodine
PH range: 5.6

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL12-210.9795
SYNCHROTRONSSRL BL11-120.9789, 0.9794,0.9184
Detector
TypeIDDetectorDate
PSI PILATUS 6M1PIXELFeb 3, 2014
PSI PILATUS 6M2PIXELApr 12, 2014
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si (111)MADMx-ray1
2Si (111)MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97891
30.97941
40.91841
ReflectionResolution: 2.5→25 Å / Num. obs: 32405 / % possible obs: 99.2 % / Redundancy: 4.7 % / Rsym value: 0.08 / Net I/σ(I): 10.8
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 1.9 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→24.902 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.92 / Stereochemistry target values: ML
Details: It is noted that the quality of the electron density around region of a tetrapeptide, Gly47-Pro48-Gly49-Pro50 was not good enough to determine the absolute conformation of CIS- or TRANS- ...Details: It is noted that the quality of the electron density around region of a tetrapeptide, Gly47-Pro48-Gly49-Pro50 was not good enough to determine the absolute conformation of CIS- or TRANS-peptide geometry in the protein structure.
RfactorNum. reflection% reflectionSelection details
Rfree0.2481 1998 6.17 %Random selection
Rwork0.1934 ---
obs0.1968 32396 99.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→24.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6575 0 13 130 6718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136732
X-RAY DIFFRACTIONf_angle_d1.369277
X-RAY DIFFRACTIONf_dihedral_angle_d13.3552505
X-RAY DIFFRACTIONf_chiral_restr0.0621135
X-RAY DIFFRACTIONf_plane_restr0.0091213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.56250.36041380.29022107X-RAY DIFFRACTION99
2.5625-2.63170.37521410.29742156X-RAY DIFFRACTION99
2.6317-2.70910.39151420.27612176X-RAY DIFFRACTION100
2.7091-2.79640.33541410.26182126X-RAY DIFFRACTION100
2.7964-2.89620.29741410.26042155X-RAY DIFFRACTION100
2.8962-3.0120.32211430.24672159X-RAY DIFFRACTION99
3.012-3.14880.30191410.22322151X-RAY DIFFRACTION99
3.1488-3.31450.28571400.21312132X-RAY DIFFRACTION98
3.3145-3.52160.25861450.20622189X-RAY DIFFRACTION100
3.5216-3.79260.25631420.19942182X-RAY DIFFRACTION99
3.7926-4.17270.23071440.16182185X-RAY DIFFRACTION99
4.1727-4.77280.17231430.14262168X-RAY DIFFRACTION98
4.7728-5.99930.18511460.14472224X-RAY DIFFRACTION99
5.9993-24.90290.20351510.16642288X-RAY DIFFRACTION99

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