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- PDB-6msv: Structure of the 6th type III domain from human fibronectin -

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Basic information

Entry
Database: PDB / ID: 6msv
TitleStructure of the 6th type III domain from human fibronectin
ComponentsFibronectin
KeywordsCELL 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 / 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 / Signaling by ALK fusions and activated point mutants / basement membrane / ECM proteoglycans / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of axon extension / Integrin cell surface interactions / Nuclear events stimulated by ALK signaling in cancer / collagen binding / extracellular matrix / Degradation of the extracellular matrix / Integrin signaling / substrate adhesion-dependent cell spreading / cell-matrix adhesion / regulation of ERK1 and ERK2 cascade / platelet alpha granule lumen / integrin-mediated signaling pathway / Post-translational protein phosphorylation / acute-phase response / Cell surface interactions at the vascular wall / regulation of protein phosphorylation / Signaling by high-kinase activity BRAF mutants / wound healing / 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) / 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 / 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 / collagen-containing extracellular matrix / angiogenesis / blood microparticle / Interleukin-4 and Interleukin-13 signaling / protease binding / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLoa, S. / 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)R01GM114657 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103546 United States
CitationJournal: To Be Published
Title: Structure of the 6th type III domain from human fibronectin
Authors: Loa, S. / Mou, T.C. / Sprang, S.R. / Briknarova, K.
History
DepositionOct 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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
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
K: Fibronectin
L: Fibronectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,58214
Polymers116,39812
Non-polymers1842
Water2,666148
1
A: Fibronectin


Theoretical massNumber of molelcules
Total (without water)9,7001
Polymers9,7001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fibronectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7922
Polymers9,7001
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fibronectin


Theoretical massNumber of molelcules
Total (without water)9,7001
Polymers9,7001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Fibronectin


Theoretical massNumber of molelcules
Total (without water)9,7001
Polymers9,7001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Fibronectin


Theoretical massNumber of molelcules
Total (without water)9,7001
Polymers9,7001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Fibronectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7922
Polymers9,7001
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Fibronectin


Theoretical massNumber of molelcules
Total (without water)9,7001
Polymers9,7001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Fibronectin


Theoretical massNumber of molelcules
Total (without water)9,7001
Polymers9,7001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Fibronectin


Theoretical massNumber of molelcules
Total (without water)9,7001
Polymers9,7001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Fibronectin


Theoretical massNumber of molelcules
Total (without water)9,7001
Polymers9,7001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Fibronectin


Theoretical massNumber of molelcules
Total (without water)9,7001
Polymers9,7001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Fibronectin


Theoretical massNumber of molelcules
Total (without water)9,7001
Polymers9,7001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
A: Fibronectin
G: Fibronectin
H: Fibronectin
J: Fibronectin


Theoretical massNumber of molelcules
Total (without water)38,7994
Polymers38,7994
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-25 kcal/mol
Surface area14810 Å2
MethodPISA
14
B: Fibronectin
D: Fibronectin
F: Fibronectin
L: Fibronectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9846
Polymers38,7994
Non-polymers1842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-22 kcal/mol
Surface area15170 Å2
MethodPISA
15
C: Fibronectin
E: Fibronectin
I: Fibronectin
K: Fibronectin


Theoretical massNumber of molelcules
Total (without water)38,7994
Polymers38,7994
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-24 kcal/mol
Surface area14450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.520, 79.460, 80.886
Angle α, β, γ (deg.)112.33, 95.88, 94.48
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 9699.831 Da / Num. of mol.: 12
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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.0 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.3→26.64 Å / Num. obs: 46905 / % possible obs: 90.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 41.3 Å2 / Rsym value: 0.08 / Net I/σ(I): 13.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4387 / Rsym value: 0.66 / % possible all: 78.1

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DFT

5dft


Resolution: 2.4→26.64 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 0.1 / Phase error: 35.62
RfactorNum. reflection% reflection
Rfree0.295 1680 4.25 %
Rwork0.2353 --
obs0.2379 39570 91.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→26.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7667 0 12 148 7827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047846
X-RAY DIFFRACTIONf_angle_d0.70210779
X-RAY DIFFRACTIONf_dihedral_angle_d9.4994749
X-RAY DIFFRACTIONf_chiral_restr0.0531303
X-RAY DIFFRACTIONf_plane_restr0.0061401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.47060.40061230.36352902X-RAY DIFFRACTION84
2.4706-2.55030.39121280.34082955X-RAY DIFFRACTION85
2.5503-2.64130.38371370.31782928X-RAY DIFFRACTION86
2.6413-2.7470.4041320.32582959X-RAY DIFFRACTION86
2.747-2.87190.34231390.29993122X-RAY DIFFRACTION90
2.8719-3.02310.4011440.27143188X-RAY DIFFRACTION93
3.0231-3.21220.30071420.24613245X-RAY DIFFRACTION94
3.2122-3.45970.31581460.24063298X-RAY DIFFRACTION96
3.4597-3.8070.27811450.21763285X-RAY DIFFRACTION97
3.807-4.35580.2611490.21873344X-RAY DIFFRACTION97
4.3558-5.480.26141460.18193323X-RAY DIFFRACTION97
5.48-26.64110.24361490.20533341X-RAY DIFFRACTION97

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