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(-) Description

Title :  NMR STRUCTURE OF THE FIBRONECTIN EDA DOMAIN, NMR, 20 STRUCTURES
 
Authors :  T. Niimi, M. Osawa, N. Yamaji, K. Yasunaga, H. Sakashita, T. Mase, A. Tanaka, S. Fujita
Date :  22 May 01  (Deposition) - 06 Feb 02  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Eda, Fibronectin, Typeiii Domain, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Niimi, M. Osawa, N. Yamaji, K. Yasunaga, H. Sakashita, T. Mase, A. Tanaka, S. Fujita
Nmr Structure Of Human Fibronectin Eda.
J. Biomol. Nmr V. 21 281 2001
PubMed-ID: 11775745  |  Reference-DOI: 10.1023/A:1012947209393
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FIBRONECTIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: EXTRA DOMAIN 2 (RESIDUES 1631-1724)
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1J8K)

(-) Sites  (0, 0)

(no "Site" information available for 1J8K)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J8K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1J8K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J8K)

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FN3PS50853 Fibronectin type-III domain profile.FINC_HUMAN610-702
722-812
813-904
999-1088
909-998
1269-1361
1176-1266
1089-1175
1450-1543
1362-1449
1544-1635
1724-1817
1636-1723
1905-1995
1818-1904
2103-2197		  2-
-
-
-
-
-
-
-
-
-
-
A:94-94
A:6-93
-
-
-

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000003596711cENSE00001245714chr2:216300791-216300378414FINC_HUMAN1-50500--
1.2ENST000003596712ENSE00001342487chr2:216299547-216299419129FINC_HUMAN50-93440--
1.3ENST000003596713ENSE00001146266chr2:216298184-216298047138FINC_HUMAN93-139470--
1.4ENST000003596714ENSE00001342465chr2:216296687-216296556132FINC_HUMAN139-183450--
1.5ENST000003596715ENSE00001342461chr2:216295575-216295438138FINC_HUMAN183-229470--
1.6ENST000003596716ENSE00001146236chr2:216293061-216292903159FINC_HUMAN229-282540--
1.7ENST000003596717ENSE00001245674chr2:216290008-216289817192FINC_HUMAN282-346650--
1.8ENST000003596718ENSE00001245669chr2:216289048-216288869180FINC_HUMAN346-406610--
1.9ENST000003596719ENSE00001146209chr2:216288249-216288073177FINC_HUMAN406-465600--
1.10ENST0000035967110ENSE00001245657chr2:216286966-216286814153FINC_HUMAN465-516520--
1.11bENST0000035967111bENSE00001342442chr2:216285524-216285396129FINC_HUMAN516-559440--
1.12bENST0000035967112bENSE00001146180chr2:216284108-216283965144FINC_HUMAN559-607490--
1.13aENST0000035967113aENSE00001223232chr2:216279681-216279560122FINC_HUMAN607-647410--
1.14aENST0000035967114aENSE00001342433chr2:216274837-216274657181FINC_HUMAN648-708610--
1.14cENST0000035967114cENSE00001342429chr2:216274462-216274286177FINC_HUMAN708-767600--
1.15bENST0000035967115bENSE00001146152chr2:216273149-216273021129FINC_HUMAN767-810440--
1.16ENST0000035967116ENSE00001342422chr2:216272920-21627283190FINC_HUMAN810-840310--
1.17ENST0000035967117ENSE00001342419chr2:216272044-216271850195FINC_HUMAN840-905660--
1.18ENST0000035967118ENSE00001342416chr2:216271233-216270961273FINC_HUMAN905-996920--
1.19ENST0000035967119ENSE00001146122chr2:216269378-216269112267FINC_HUMAN996-1085900--
1.20ENST0000035967120ENSE00001146112chr2:216264074-21626398095FINC_HUMAN1085-1116320--
1.21bENST0000035967121bENSE00000965892chr2:216262571-216262403169FINC_HUMAN1117-1173570--
1.22ENST0000035967122ENSE00001146105chr2:216261946-21626186087FINC_HUMAN1173-1202300--
1.23ENST0000035967123ENSE00001342408chr2:216259442-216259251192FINC_HUMAN1202-1266650--
1.25cENST0000035967125cENSE00001146412chr2:216256537-216256355183FINC_HUMAN1266-1327620--
1.26ENST0000035967126ENSE00001342403chr2:216253024-21625293590FINC_HUMAN1327-1357310--
1.27aENST0000035967127aENSE00001342401chr2:216251681-216251412270FINC_HUMAN1357-1447910--
1.28aENST0000035967128aENSE00001342398chr2:216249699-216249583117FINC_HUMAN1447-1486400--
1.28cENST0000035967128cENSE00001146062chr2:216248907-216248743165FINC_HUMAN1486-1541560--
1.29ENST0000035967129ENSE00001342394chr2:216248206-216248051156FINC_HUMAN1541-1593530--
1.30aENST0000035967130aENSE00001146049chr2:216247048-216246935114FINC_HUMAN1593-1631391A:1-11
1.30fENST0000035967130fENSE00001245789chr2:216245803-216245534270FINC_HUMAN1631-1721911A:1-9191
1.30hENST0000035967130hENSE00001342389chr2:216244040-216243853188FINC_HUMAN1721-1783631A:91-944
1.31ENST0000035967131ENSE00001342388chr2:216242985-21624289888FINC_HUMAN1784-1813300--
1.32ENST0000035967132ENSE00001245772chr2:216241397-216241221177FINC_HUMAN1813-1872600--
1.33cENST0000035967133cENSE00001342219chr2:216240441-21624035290FINC_HUMAN1872-1902310--
1.34ENST0000035967134ENSE00001145995chr2:216240116-216239937180FINC_HUMAN1902-1962610--
1.35ENST0000035967135ENSE00001145987chr2:216238134-21623804590FINC_HUMAN1962-1992310--
1.36dENST0000035967136dENSE00001145978chr2:216237098-216236632467FINC_HUMAN1992-21471560--
1.37dENST0000035967137dENSE00001342210chr2:216235155-216235017139FINC_HUMAN2148-2194470--
1.38aENST0000035967138aENSE00001603320chr2:216232750-216232586165FINC_HUMAN2194-2249560--
1.39cENST0000035967139cENSE00001598844chr2:216230353-216230228126FINC_HUMAN2249-2291430--
1.40aENST0000035967140aENSE00001649647chr2:216229708-216229602107FINC_HUMAN2291-2326360--
1.41bENST0000035967141bENSE00001740966chr2:216226802-216226692111FINC_HUMAN2327-2363370--
1.42fENST0000035967142fENSE00001696465chr2:216226349-2162251811169FINC_HUMAN2364-2386230--

(-) Sequences/Alignments

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
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:94
 aligned with FINC_HUMAN | P02751 from UniProtKB/Swiss-Prot  Length:2386

    Alignment length:94
                                  1640      1650      1660      1670      1680      1690      1700      1710      1720    
          FINC_HUMAN   1631 NIDRPKGLAFTDVDVDSIKIAWESPQGQVSRYRVTYSSPEDGIHELFPAPDGEEDTAELQGLRPGSEYTVSVVALHDDMESQPLIGTQSTAIPA 1724
               SCOP domains d1j8ka_ A: Fibronectin, different Fn3 modules                                                  SCOP domains
               CATH domains 1j8kA00 A:1-94 Immunoglobulins                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee..eeeee..........eeeeeee...eeeee.........eeee.......eeeeeeee.........eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE FN3  FN3  PDB: A:6-93 UniProt: 1636-1723                                                     F PROSITE
           Transcript 1 (1) 1-----------------------------------------------------------------------------------------1.30 Transcript 1 (1)
           Transcript 1 (2) Exon 1.30f  PDB: A:1-91 UniProt: 1631-1721                                                 --- Transcript 1 (2)
                1j8k A    1 NIDRPKGLAFTDVDVDSIKIAWESPQGQVSRYRVTYSSPEDGIHELFPAPDGEEDTAELQGLRPGSEYTVSVVALHDDMESQPLIGTQSTAIPA   94
                                    10        20        30        40        50        60        70        80        90
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

NMR Structure
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J8K)

(-) Gene Ontology  (63, 63)

NMR Structure(hide GO term definitions)
Chain A   (FINC_HUMAN | P02751)
molecular function
    GO:0005518    collagen binding    Interacting selectively and non-covalently with collagen, a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%).
    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:0022617    extracellular matrix disassembly    A process that results in the breakdown of the extracellular matrix.
    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:0050900    leukocyte migration    The movement of a leukocyte within or between different tissues and organs of the body.
    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:0002576    platelet degranulation    The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
    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:0031093    platelet alpha granule lumen    The volume enclosed by the membrane of the platelet alpha granule.
    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.

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(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        FINC_HUMAN | P02751: 1e88 1e8b 1fbr 1fna 1fnf 1fnh 1o9a 1oww 1q38 1qgb 1qo6 1ttf 1ttg 2cg6 2cg7 2ck2 2cku 2ec3 2fn2 2fnb 2gee 2h41 2h45 2ha1 2mnu 2n1k 2ocf 2rky 2rkz 2rl0 3cal 3ejh 3gxe 3m7p 3mql 3r8q 3t1w 3zrz 4gh7 4je4 4jeg 4lxo 4mmx 4mmy 4mmz 4pz5 5dc0 5dc4 5dc9 5dft 5j6z 5j7c

(-) Related Entries Specified in the PDB File

5027 THE CHEMICAL SHIFT TABLE OF FIBRONECTIN