1MFN - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   SOLUTION NMR STRUCTURE OF LINKED CELL ATTACHMENT MODULES OF MOUSE FIBRONECTIN CONTAINING THE RGD AND SYNERGY REGIONS, 20 STRUCTURES

Authors :   V. Copie, Y. Tomita, S. K. Akiyama, S. Aota, K. M. Yamada, R. M. Venable, R. W. Pastor, S. Krueger, D. A. Torchia

Date :   27 Jan 98 (Deposition) - 29 Apr 98 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Cell Adhesion Protein, Rgd, Extracellular Matrix, Heparin- Binding, Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. Copie, Y. Tomita, S. K. Akiyama, S. Aota, K. M. Yamada, R. M. Venable, R. W. Pastor, S. Krueger, D. A. Torchia
Solution Structure And Dynamics Of Linked Cell Attachment Modules Of Mouse Fibronectin Containing The Rgd And Synergy Regions: Comparison With The Human Fibronectin Crystal Structure.
J. Mol. Biol. V. 277 663 1998
PubMed-ID: 9533887 | Reference-DOI: 10.1006/JMBI.1998.1616
(for further references see the PDB file header)

Molecule 1 - FIBRONECTIN
	Cell Line	:	BL21
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	BL21
	Expression System Strain	:	BL21 (DE3) PLYSS
	Expression System Taxid	:	562
	Expression System Vector	:	PRSET
	Fragment	:	184 AMINO ACID FRAGMENT, 9TH AND 10TH TYPE-III REPEATS
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1MFN)

NMR Structure (2, 2)

No.	Name	Evidence	Residues	Description
1	RGD	UNKNOWN	ARG A:168 , GLY A:169 , ASP A:170	CELL ADHESION SITE.
2	SGY	UNKNOWN	PRO A:51 , PRO A:52 , SER A:53 , ARG A:54 , ASN A:55	CELL ADHESION SYNERGETIC SITE.

(no "SS Bond" information available for 1MFN)

(no "Cis Peptide Bond" information available for 1MFN)

(no "SAP(SNP)/Variant" information available for 1MFN)

NMR Structure (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FN3	PS50853	Fibronectin type-III domain profile.	FINC_MOUSE	610-717 721-811 812-903 998-1087 908-997 1175-1269 1088-1174 1540-1633 1359-1451 1270-1358 1452-1539 1634-1725 1814-1907 1726-1813 1995-2085 1908-1994 2193-2287	2	- - - - - - - A:94-184 - - A:6-93 - - - - - -

(no "Exon" information available for 1MFN)

NMR Structure

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:184
 aligned with FINC_MOUSE | P11276 from UniProtKB/Swiss-Prot  Length:2477

    Alignment length:184
                                  1456      1466      1476      1486      1496      1506      1516      1526      1536      1546      1556      1566      1576      1586      1596      1606      1616      1626    
          FINC_MOUSE   1447 GLDSPTGFDSSDITANSFTVHWVAPRAPITGYIIRHHAEHSVGRPRQDRVPPSRNSITLTNLNPGTEYVVSIIAVNGREESPPLIGQQATVSDIPRDLEVIASTPTSLLISWEPPAVSVRYYRITYGETGGNSPVQEFTVPGSKSTATINNIKPGADYTITLYAVTGRGDSPASSKPVSINYKT 1630
               SCOP domains d1mfna1 A:1-92 Fibronectin, different Fn3 modules                                           d1mfna2 A:93-184 Fibronectin, different Fn3 modules                                          SCOP domains
               CATH domains 1mfnA01 A:1-91 Immunoglobulins                                                             1mfnA02 A:92-184 Immunoglobulins                                                              CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------fn3-1mfnA01 A:93-174                                                              ---------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------fn3-1mfnA02 A:93-174                                                              ---------- Pfam domains (2)
         Sec.struct. author ........eeeee...eeeee.........eeeeeeee.......eeeee.....eeeee.....eeeeeeeeee........eeeeeee........eeeeee..eeeee.........eeeeeeee.......eeeee.....eee.......eeeeeeeeee............eeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE FN3  FN3  PDB: A:6-93 UniProt: 1452-1539                                                     FN3  PDB: A:94-184 UniProt: 1540-1633                                                       PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1mfn A    1 GLDSPTGFDSSDITANSFTVHWVAPRAPITGYIIRHHAEHSVGRPRQDRVPPSRNSITLTNLNPGTEYVVSIIAVNGREESPPLIGQQATVSDIPRDLEVIASTPTSLLISWEPPAVSVRYYRITYGETGGNSPVQEFTVPGSKSTATINNIKPGADYTITLYAVTGRGDSPASSKPVSINYKT  184
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Fibronectin type III (212)

Family: Fibronectin type III (180)

Protein domain: Fibronectin, different Fn3 modules (12)

Mouse (Mus musculus) [TaxId: 10090] (2)

1a	d1mfna1	A:1-92
1b	d1mfna2	A:93-184

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

House mouse (Mus musculus) (616)

1a	1mfnA02	A:92-184
1b	1mfnA01	A:1-91

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: E-set (290)

Family: fn3 (66)

Mus musculus (Mouse) (7)

1a	fn3-1mfnA01	A:93-174
1b	fn3-1mfnA02	A:93-174

NMR Structure(hide GO term definitions)

Chain A (FINC_MOUSE | P11276)

molecular function
	GO:0008201	heparin binding	Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0005178	integrin binding	Interacting selectively and non-covalently with an integrin.
	GO:0045340	mercury ion binding	Interacting selectively and non-covalently with mercury (Hg) ions.
	GO:0016504	peptidase activator activity	Binds to and increases the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
	GO:0002020	protease binding	Interacting selectively and non-covalently with any protease or peptidase.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0006953	acute-phase response	An acute inflammatory response that involves non-antibody proteins whose concentrations in the plasma increase in response to infection or injury of homeothermic animals.
	GO:0001525	angiogenesis	Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
	GO:0007161	calcium-independent cell-matrix adhesion	The binding of a cell to the extracellular matrix via adhesion molecules that do not require the presence of calcium for the interaction.
	GO:0001775	cell activation	A change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand.
	GO:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
	GO:0007160	cell-matrix adhesion	The binding of a cell to the extracellular matrix via adhesion molecules.
	GO:0007044	cell-substrate junction assembly	The aggregation, arrangement and bonding together of a set of components to form a junction between a cell and its substrate.
	GO:0071773	cellular response to BMP stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a bone morphogenetic protein (BMP) stimulus.
	GO:0071333	cellular response to glucose stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucose stimulus.
	GO:0071347	cellular response to interleukin-1	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interleukin-1 stimulus.
	GO:0071222	cellular response to lipopolysaccharide	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
	GO:0071288	cellular response to mercury ion	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mercury ion stimulus.
	GO:0036120	cellular response to platelet-derived growth factor stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a platelet-derived growth factor stimulus.
	GO:0071380	cellular response to prostaglandin E stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a prostagladin E stimulus.
	GO:0071560	cellular response to transforming growth factor beta stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a transforming growth factor beta stimulus.
	GO:0035924	cellular response to vascular endothelial growth factor stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a vascular endothelial growth factor stimulus.
	GO:0035987	endodermal cell differentiation	The process in which a relatively unspecialized cell acquires the specialized features of an endoderm cell, a cell of the inner of the three germ layers of the embryo.
	GO:0030198	extracellular matrix organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
	GO:0008347	glial cell migration	The orderly movement of a glial cell, non-neuronal cells that provide support and nutrition, maintain homeostasis, form myelin, and participate in signal transmission in the nervous system.
	GO:0033622	integrin activation	The aggregation, arrangement and bonding together of an integrin, a heterodimeric adhesion receptor formed by the non-covalent association of particular alpha and beta subunits, that lead to the increased affinity of the integrin for its extracellular ligands.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:2001202	negative regulation of transforming growth factor-beta secretion	Any process that stops, prevents or reduces the frequency, rate or extent of transforming growth factor-beta secretion.
	GO:0018149	peptide cross-linking	The formation of a covalent cross-link between or within protein chains.
	GO:0045773	positive regulation of axon extension	Any process that activates or increases the frequency, rate or extent of axon extension.
	GO:0030335	positive regulation of cell migration	Any process that activates or increases the frequency, rate or extent of cell migration.
	GO:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:0050921	positive regulation of chemotaxis	Any process that activates or increases the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient.
	GO:0048146	positive regulation of fibroblast proliferation	Any process that activates or increases the frequency, rate or extent of multiplication or reproduction of fibroblast cells.
	GO:0010628	positive regulation of gene expression	Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0010952	positive regulation of peptidase activity	Any process that increases the frequency, rate or extent of peptidase activity, the hydrolysis of peptide bonds within proteins.
	GO:1904237	positive regulation of substrate-dependent cell migration, cell attachment to substrate	Any process that activates or increases the frequency, rate or extent of substrate-dependent cell migration, cell attachment to substrate.
	GO:0070372	regulation of ERK1 and ERK2 cascade	Any process that modulates the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
	GO:0008360	regulation of cell shape	Any process that modulates the surface configuration of a cell.
	GO:0001932	regulation of protein phosphorylation	Any process that modulates the frequency, rate or extent of addition of phosphate groups into an amino acid in a protein.
	GO:0051384	response to glucocorticoid	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucocorticoid stimulus. Glucocorticoids are hormonal C21 corticosteroids synthesized from cholesterol with the ability to bind with the cortisol receptor and trigger similar effects. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects.
	GO:0002931	response to ischemia	Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a inadequate blood supply.
	GO:0010193	response to ozone	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ozone stimulus.
	GO:0009611	response to wounding	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism.
	GO:0034446	substrate adhesion-dependent cell spreading	The morphogenetic process that results in flattening of a cell as a consequence of its adhesion to a substrate.
	GO:0042060	wound healing	The series of events that restore integrity to a damaged tissue, following an injury.
cellular component
	GO:0016324	apical plasma membrane	The region of the plasma membrane located at the apical end of the cell.
	GO:0005605	basal lamina	A thin sheet of proteoglycans and glycoproteins, especially laminin, secreted by cells as an extracellular matrix.
	GO:0005604	basement membrane	A thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers.
	GO:0072562	blood microparticle	A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
	GO:0005793	endoplasmic reticulum-Golgi intermediate compartment	A complex system of membrane-bounded compartments located between endoplasmic reticulum (ER) and the Golgi complex, with a distinctive membrane protein composition; involved in ER-to-Golgi and Golgi-to-ER transport.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0031012	extracellular matrix	A structure lying external to one or more cells, which provides structural support for cells or tissues.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0005577	fibrinogen complex	A highly soluble, elongated protein complex found in blood plasma and involved in clot formation. It is converted into fibrin monomer by the action of thrombin. In the mouse, fibrinogen is a hexamer, 46 nm long and 9 nm maximal diameter, containing two sets of nonidentical chains (alpha, beta, and gamma) linked together by disulfide bonds.
	GO:0005578	proteinaceous extracellular matrix	A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

NMR Structure
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	1mfn
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(no "Related Entries Specified in the PDB File" available for 1MFN)

Description

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Ligands, Modified Residues, Ions (0, 0)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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