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(-) Description

Title :  CRYSTAL STRUCTURE OF RACEMIC VILLIN HEADPIECE SUBDOMAIN CRYSTALLIZED IN SPACE GROUP P-1
 
Authors :  D. E. Mortenson, K. A. Satyshur, S. H. Gellman, K. T. Forest
Date :  11 Sep 11  (Deposition) - 25 Jan 12  (Release) - 22 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  D  (1x)
Keywords :  Racemate, Quasi-Racemate, D-Amino Acids, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. E. Mortenson, K. A. Satyshur, I. A. Guzei, K. T. Forest, S. H. Gellman
Quasiracemic Crystallization As A Tool To Assess The Accommodation Of Noncanonical Residues In Nativelike Protei Conformations.
J. Am. Chem. Soc. V. 134 2473 2012
PubMed-ID: 22280019  |  Reference-DOI: 10.1021/JA210045S

(-) Compounds

Molecule 1 - VILLIN-1
    ChainsA, D
    EngineeredYES
    FragmentHEADPIECE SUBDOMAIN (UNP RESIDUES 792-826)
    MutationYES
    Organism CommonCHICKEN
    Organism ScientificGALLUS GALLUS
    Organism Taxid9031
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AD
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) D

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3TRW)

(-) Sites  (0, 0)

(no "Site" information available for 3TRW)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TRW)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3TRW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TRW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3TRW)

(-) Exons   (0, 0)

(no "Exon" information available for 3TRW)

(-) Sequences/Alignments

Asymmetric 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:34
 aligned with VILI_CHICK | P02640 from UniProtKB/Swiss-Prot  Length:826

    Alignment length:34
                                   801       811       821    
           VILI_CHICK   792 LSDEDFKAVFGMTRSAFANLPLWKQQNLKKEKGL 825
               SCOP domains ---------------------------------- SCOP domains
               CATH domains ---------------------------------- CATH domains
               Pfam domains ---------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.hhhhhh..hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------- PROSITE
                 Transcript ---------------------------------- Transcript
                 3trw A   1 LSDEDFKAVFGMTRSAFANLPLAKQQHLKKEKGL  34
                                    10        20        30    

Chain D from PDB  Type:PROTEIN  Length:34
 aligned with VILI_CHICK | P02640 from UniProtKB/Swiss-Prot  Length:826

    Alignment length:34
                                   801       811       821    
           VILI_CHICK   792 LSDEDFKAVFGMTRSAFANLPLWKQQNLKKEKGL 825
               SCOP domains ---------------------------------- SCOP domains
               CATH domains ---------------------------------- CATH domains
               Pfam domains ---------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.hhhhhh..hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------- PROSITE
                 Transcript ---------------------------------- Transcript
                 3trw D   1 LSDEDFKAVFGMTRSAFANLPLAKQQHLKKEKGL  34
                                    10        20        30    

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (0, 0)

(no "SCOP Domain" information available for 3TRW)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TRW)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TRW)

(-) Gene Ontology  (36, 36)

Asymmetric Unit(hide GO term definitions)
Chain A,D   (VILI_CHICK | P02640)
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:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0043027    cysteine-type endopeptidase inhibitor activity involved in apoptotic process    Stops, prevents or reduces the activity of a cysteine-type endopeptidase involved in the apoptotic process.
    GO:0035727    lysophosphatidic acid binding    Interacting selectively and non-covalently with lysophosphatidic acid (LPA), a phospholipid derivative that acts as a potent mitogen due to its activation of high-affinity G-protein-coupled receptors.
    GO:0005546    phosphatidylinositol-4,5-bisphosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-4,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' and 5' positions.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0051693    actin filament capping    The binding of a protein or protein complex to the end of an actin filament, thus preventing the addition, exchange or removal of further actin subunits.
    GO:0030042    actin filament depolymerization    Disassembly of actin filaments by the removal of actin monomers from a filament.
    GO:0030041    actin filament polymerization    Assembly of actin filaments by the addition of actin monomers to a filament.
    GO:0051014    actin filament severing    The process in which an actin filament is broken down into smaller filaments.
    GO:0045010    actin nucleation    The initial step in the formation of an actin filament, in which actin monomers combine to form a new filament. Nucleation is slow relative to the subsequent addition of more monomers to extend the filament.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0071364    cellular response to epidermal 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 an epidermal growth factor stimulus.
    GO:0035729    cellular response to hepatocyte 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 hepatocyte growth factor stimulus.
    GO:0060327    cytoplasmic actin-based contraction involved in cell motility    The actin filament-based movement by which cytoplasmic actin filaments slide past one another resulting in a contraction that propels the cell from one place to another.
    GO:0007010    cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
    GO:0007173    epidermal growth factor receptor signaling pathway    A series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor EGFR (ERBB1) on the surface of a cell. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0043154    negative regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of a cysteine-type endopeptidase activity involved in the apoptotic process.
    GO:0032233    positive regulation of actin filament bundle assembly    Any process that activates or increases the frequency, rate or extent of the assembly of actin filament bundles.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:0010634    positive regulation of epithelial cell migration    Any process that activates or increases the frequency, rate or extent of epithelial cell migration.
    GO:0051125    regulation of actin nucleation    Any process that modulates the frequency, rate or extent of actin nucleation, the initial step in the formation of an actin filament in which actin monomers combine to form a new filament.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:2000392    regulation of lamellipodium morphogenesis    Any process that modulates the frequency, rate or extent of lamellipodium morphogenesis.
    GO:0061041    regulation of wound healing    Any process that modulates the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury.
    GO:0009617    response to bacterium    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 from a bacterium.
cellular component
    GO:0032432    actin filament bundle    An assembly of actin filaments that are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    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:0030175    filopodium    Thin, stiff, actin-based protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal or dendritic growth cone, or a dendritic shaft.
    GO:0032433    filopodium tip    The end of a filopodium distal to the body of the cell.
    GO:0030027    lamellipodium    A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments.
    GO:0005902    microvillus    Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells.
    GO:0001726    ruffle    Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork.

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 Related Entries

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

UniProtKB/Swiss-Prot
        VILI_CHICK | P026401qqv 1vii 1wy3 1wy4 1yrf 1yri 1yu5 1yu7 1yu8 2f4k 2jm0 2llf 2ppz 2rjv 2rjw 2rjx 2rjy 2vik 2vil 3mya 3myc 3mye 3nkj 3tjw 3trv 3try 4cz3 4cz4 5i1n 5i1o 5i1p 5i1s

(-) Related Entries Specified in the PDB File

3tjw 3trv 3try