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Title :  STRUCTURAL GENOMICS OF CAENORHABDITIS ELEGANS: TROPOMODULIN C-TERMINAL DOMAIN
 
Authors :  J. Symersky, S. Lu, S. Li, L. Chen, E. Meehan, M. Luo, S. Qiu, R. J. Bunzel, D. Luo, A. Arabashi, L. A. Nagy, G. Lin, W. C. -H. Luan, M. Carson, R. Gray W. Huang, Southeast Collaboratory For Structural Genomics (Secsg)
Date :  28 May 03  (Deposition) - 10 Jun 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics; Tropomodulin, Psi, Protein Structure Initiative, Southeast Collaboratory For Structural Genomics, Secsg, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Lu, J. Symersky, S. Li, M. Carson, L. Chen, E. Meehan, M. Luo
Structural Genomics Of Caenorhabditis Elegans: Crystal Structure Of The Tropomodulin C-Terminal Domain
Proteins V. 56 384 2004
PubMed-ID: 15211521  |  Reference-DOI: 10.1002/PROT.10597
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TROPOMODULIN TMD-1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN
    Organism Scientific: CAENORHABDITIS ELEGANS
    Organism Taxid: 6239
    Synonym: TMD-1;
TROPOMODULIN PROTEIN 1, ISOFORM A

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

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(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

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(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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:167
 aligned with TMOD_CAEEL | O01479 from UniProtKB/Swiss-Prot  Length:392

    Alignment length:167
                                   231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       
           TMOD_CAEEL   222 TDVESCINRLREDDTDLKEVNINNMKRVSKERIRSLIEAACNSKHIEKFSLANTAISDSEARGLIELIETSPSLRVLNVESNFLTPELLARLLRSTLVTQSIVEFKADNQRQSVLGNQVEMDMMMAIEENESLLRVGISFASMEARHRVSEALERNYERVRLRRLGK 388
               SCOP domains d1pgva_ A: Tropomodulin C-terminal domain                                                                                                                               SCOP domains
               CATH domains 1pgvA00 A:222-388 Ribonuclease Inhibitor                                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh......eee.......hhhhhhhhhhhhh......eee......hhhhhhhhhhhhhhh....eee......hhhhhhhhhhhh.......eee.........hhhhhhhhhhhhhhh....eee....hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pgv A 222 TDVESCINRLREDDTDLKEVNINNMKRVSKERIRSLIEAACNSKHIEKFSLANTAISDSEARGLIELIETSPSLRVLNVESNFLTPELLARLLRSTLVTQSIVEFKADNQRQSVLGNQVEMDMMMAIEENESLLRVGISFASMEARHRVSEALERNYERVRLRRLGK 388
                                   231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381
   Legend:   → Mismatch (orange background)
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  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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TMOD_CAEEL | O01479)
molecular function
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0051015    actin filament binding    Interacting selectively and non-covalently with an actin filament, also known as F-actin, a helical filamentous polymer of globular G-actin subunits.
    GO:0005523    tropomyosin binding    Interacting selectively and non-covalently with tropomyosin, a protein associated with actin filaments both in cytoplasm and, in association with troponin, in the thin filament of striated muscle.
biological process
    GO:0009792    embryo development ending in birth or egg hatching    The process whose specific outcome is the progression of an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell.
    GO:0040011    locomotion    Self-propelled movement of a cell or organism from one location to another.
    GO:0071689    muscle thin filament assembly    The aggregation, arrangement and bonding together of proteins to form the actin-based thin filaments of myofibrils in striated muscle.
    GO:0030835    negative regulation of actin filament depolymerization    Any process that stops, prevents, or reduces the frequency, rate or extent of actin depolymerization.
    GO:0002119    nematode larval development    The process whose specific outcome is the progression of the nematode larva over time, from its formation to the mature structure. Nematode larval development begins with the newly hatched first-stage larva (L1) and ends with the end of the last larval stage (for example the fourth larval stage (L4) in C. elegans). Each stage of nematode larval development is characterized by proliferation of specific cell lineages and an increase in body size without alteration of the basic body plan. Nematode larval stages are separated by molts in which each stage-specific exoskeleton, or cuticle, is shed and replaced anew.
    GO:0051694    pointed-end actin filament capping    The binding of a protein or protein complex to the pointed (or minus) end of an actin filament, thus preventing the addition, exchange or removal of further actin subunits.
    GO:0045214    sarcomere organization    The myofibril assembly process that results in the organization of muscle actomyosin into sarcomeres. The sarcomere is the repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0005865    striated muscle thin filament    Filaments formed of actin and associated proteins; attached to Z discs at either end of sarcomeres in myofibrils.
    GO:1990357    terminal web    An actin-rich cytoskeletal network located beneath the microvilli of the apical plasma membrane of polarized epithelial cells. In addition to actin filaments, the terminal web may contain actin-binding proteins, myosin motor proteins, and intermediate filaments. The terminal web can function as a contractile structure that influences the spatial distribution of microvilli as well as the development and morphogenesis of tissues containing polarized epithelial cells.

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 Related Entries

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(-) Related Entries Specified in the PDB File

1io0 CHICKEN TROPOMODULIN C-TERMINAL DOMAIN RELATED ID: C06A5.7 RELATED DB: TARGETDB