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(-) Description

Title :  HIGH RESOLUTION DESIGN OF A PROTEIN LOOP
 
Authors :  X. Hu, H. Wang, H. Ke, B. Kuhlman
Date :  18 Sep 07  (Deposition) - 20 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta Sheet, Loop Design, Alternative Splicing, Cell Adhesion, Coiled Coil, Egf-Like Domain, Extracellular Matrix, Glycoprotein, Phosphorylation, Polymorphism, Secreted (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Hu, H. Wang, H. Ke, B. Kuhlman
High-Resolution Design Of A Protein Loop.
Proc. Natl. Acad. Sci. Usa V. 104 17668 2007
PubMed-ID: 17971437  |  Reference-DOI: 10.1073/PNAS.0707977104
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TENASCIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21B
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 802-896
    GeneTNC, HXB
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTN, TENASCIN-C, TN-C, HEXABRACHION, CYTOTACTIN, NEURONECTIN, GMEM, JI, MYOTENDINOUS ANTIGEN, GLIOMA- ASSOCIATED-EXTRACELLULAR MATRIX ANTIGEN, GP 150-225

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2RB8)

(-) Sites  (0, 0)

(no "Site" information available for 2RB8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2RB8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2RB8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_055779D850HTENA_HUMANPolymorphism3748169AD850H

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FN3PS50853 Fibronectin type-III domain profile.TENA_HUMAN625-715
895-990
805-894
716-804
1076-1165
991-1075
1258-1350
1167-1256
1351-1439
1440-1531
1712-1801
1622-1711
1533-1621
1889-1977
1802-1888
  1-
-
A:805-893
-
-
-
-
-
-
-
-
-
-
-
-

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003507631bENSE00001898470chr9:117880439-117880261179TENA_HUMAN-00--
1.2ENST000003507632ENSE00001376978chr9:117853433-117852841593TENA_HUMAN1-1531530--
1.3ENST000003507633ENSE00000926930chr9:117849552-1178481431410TENA_HUMAN153-6234710--
1.4ENST000003507634ENSE00000926929chr9:117846751-117846488264TENA_HUMAN623-711890--
1.5ENST000003507635ENSE00000926928chr9:117845086-117844971116TENA_HUMAN711-749390--
1.6ENST000003507636ENSE00000926927chr9:117844207-117844051157TENA_HUMAN750-802531A:801-8022
1.7ENST000003507637ENSE00000926926chr9:117840491-117840222270TENA_HUMAN802-892911A:802-89291
1.8bENST000003507638bENSE00000926925chr9:117838854-117838669186TENA_HUMAN892-954631A:892-8932
1.9ENST000003507639ENSE00000722787chr9:117838400-11783831190TENA_HUMAN954-984310--
1.10aENST0000035076310aENSE00000722751chr9:117836145-117835882264TENA_HUMAN984-1072890--
1.11ENST0000035076311ENSE00000722704chr9:117827198-117826926273TENA_HUMAN1072-1163920--
1.12ENST0000035076312ENSE00000722678chr9:117826347-117826075273TENA_HUMAN1163-1254920--
1.13aENST0000035076313aENSE00000722656chr9:117825468-117825196273TENA_HUMAN1254-1345920--
1.14ENST0000035076314ENSE00000722641chr9:117822281-117822009273TENA_HUMAN1345-1436920--
1.15ENST0000035076315ENSE00000722592chr9:117819704-117819432273TENA_HUMAN1436-1527920--
1.18ENST0000035076318ENSE00000926924chr9:117810811-117810539273TENA_HUMAN1527-1618920--
1.19bENST0000035076319bENSE00000926923chr9:117808961-117808689273TENA_HUMAN1618-1709920--
1.20ENST0000035076320ENSE00000926922chr9:117804620-117804498123TENA_HUMAN1709-1750420--
1.21ENST0000035076321ENSE00000926921chr9:117803363-117803220144TENA_HUMAN1750-1798490--
1.22ENST0000035076322ENSE00000926920chr9:117800659-117800540120TENA_HUMAN1798-1838410--
1.23cENST0000035076323cENSE00000926919chr9:117798520-117798377144TENA_HUMAN1838-1886490--
1.25ENST0000035076325ENSE00000926918chr9:117797613-117797483131TENA_HUMAN1886-1929440--
1.26bENST0000035076326bENSE00000926917chr9:117793964-117793832133TENA_HUMAN1930-1974450--
1.27bENST0000035076327bENSE00000926916chr9:117792684-117792533152TENA_HUMAN1974-2024510--
1.28ENST0000035076328ENSE00000926915chr9:117791735-11779163997TENA_HUMAN2025-2057330--
1.29ENST0000035076329ENSE00000926914chr9:117788974-117788813162TENA_HUMAN2057-2111550--
1.30ENST0000035076330ENSE00000926913chr9:117786415-117786252164TENA_HUMAN2111-2165550--
1.31aENST0000035076331aENSE00001948855chr9:117783546-117782813734TENA_HUMAN2166-2201360--

(-) Sequences/Alignments

Asymmetric/Biological Unit
   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:93
 aligned with TENA_HUMAN | P24821 from UniProtKB/Swiss-Prot  Length:2201

    Alignment length:93
                                   810       820       830       840       850       860       870       880       890   
           TENA_HUMAN   801 TRLDAPSQIEVKDVTDTTALITWFKPLAEIDGIELTYGIKDVPGDRTTIDLTEDENQYSIGNLKPDTEYEVSLISRRGDMSSNPAKETFTTGL 893
               SCOP domains d2rb8a_ A: automated matches                                                                  SCOP domains
               CATH domains 2rb8A00 A:801-893 Immunoglobulins                                                             CATH domains
               Pfam domains ---fn3-2rb8A01 A:804-884                                                            --------- Pfam domains
         Sec.struct. author ......eeeeee......eeeeee.......eeeeeeee.......eeeeee....eeee.......eeeeeeeeee..ee...eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------H------------------------------------------- SAPs(SNPs)
                    PROSITE FN3 FN3  PDB: A:805-893 UniProt: 805-894                                                      PROSITE
           Transcript 1 (1) 1.-----------------------------------------------------------------------------------------1. Transcript 1 (1)
           Transcript 1 (2) -Exon 1.7  PDB: A:802-892 UniProt: 802-892                                                  - Transcript 1 (2)
                 2rb8 A 801 MRLDAPSQIEVKDVTDTTALITWMPPSQPVDGFELTYGIKDVPGDRTTIDLTEDENQYSIGNLKPDTEYEVSLISRRGDMSSNPAKETFTTGL 893
                                   810       820       830       840       850       860       870       880       890   

   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)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: E-set (290)
(-)
Family: fn3 (66)

(-) Gene Ontology  (31, 31)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TENA_HUMAN | P24821)
molecular function
    GO:0045545    syndecan binding    Interacting selectively and non-covalently with syndecan, an integral membrane proteoglycan (250-300 kDa) associated largely with epithelial cells.
biological process
    GO:0060447    bud outgrowth involved in lung branching    The process in which a region of the lung epithelium initiates an outgrowth.
    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:0071799    cellular response to prostaglandin D 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 D stimulus.
    GO:0071300    cellular response to retinoic acid    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 retinoic acid stimulus.
    GO:0071305    cellular response to vitamin D    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 vitamin D stimulus.
    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:0060739    mesenchymal-epithelial cell signaling involved in prostate gland development    Any process that mediates the transfer of information from a mesenchymal cell to an epithelial cell where it is received and interpreted contributing to the progression of the prostate gland over time.
    GO:0007162    negative regulation of cell adhesion    Any process that stops, prevents, or reduces the frequency, rate or extent of cell adhesion.
    GO:0007528    neuromuscular junction development    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a neuromuscular junction.
    GO:0031175    neuron projection development    The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    GO:0042475    odontogenesis of dentin-containing tooth    The process whose specific outcome is the progression of a dentin-containing tooth over time, from its formation to the mature structure. A dentin-containing tooth is a hard, bony organ borne on the jaw or other bone of a vertebrate, and is composed mainly of dentin, a dense calcified substance, covered by a layer of enamel.
    GO:0001649    osteoblast differentiation    The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone.
    GO:0014012    peripheral nervous system axon regeneration    The regrowth of axons outside the central nervous system (outside the brain and spinal cord) following an axonal injury.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    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:0060740    prostate gland epithelium morphogenesis    The process in which the anatomical structures of epithelia of the prostate gland are generated and organized. An epithelium consists of closely packed cells arranged in one or more layers, that covers the outer surfaces of the body or lines any internal cavity or tube.
    GO:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    GO:0045471    response to ethanol    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 an ethanol stimulus.
    GO:0071774    response to fibroblast growth factor    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 fibroblast growth factor stimulus.
    GO:0009612    response to mechanical stimulus    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 mechanical 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:0042060    wound healing    The series of events that restore integrity to a damaged tissue, following an injury.
cellular component
    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: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:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0005614    interstitial matrix    A type of extracellular matrix found in interstitial connective tissue, characterized by the presence of fibronectins, proteoglycans, and types I, III, V, VI, VII and XII collagens.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        TENA_HUMAN | P248211ten 2rbl

(-) Related Entries Specified in the PDB File

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