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(-) Description

Title :  STRUCTURE OF YEAST DOM34 : A PROTEIN RELATED TO TRANSLATION TERMINATION FACTOR ERF1 AND INVOLVED IN NO-GO DECAY.
 
Authors :  M. Graille, M. Chaillet, H. Van Tilbeurgh
Date :  14 Nov 07  (Deposition) - 22 Jan 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Translation Termination Factor, Protein Biosynthesis, Translation Regulation, Cell Division, Mrna Degradation, Nucleotide Binding, Mitosis, Meiosis, Cytoplasm, Cell Cycle, No-Go Decay (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Graille, M. Chaillet, H. Van Tilbeurgh
Structure Of Yeast Dom34: A Protein Related To Translation Termination Factor Erf1 And Involved In No-Go Decay.
J. Biol. Chem. V. 283 7145 2008
PubMed-ID: 18180287  |  Reference-DOI: 10.1074/JBC.M708224200

(-) Compounds

Molecule 1 - DOM34
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET9
    Expression System StrainROSETTA(DE3)PLYSS
    Expression System Taxid562
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    StrainS288C

 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 2VGM)

(-) Sites  (0, 0)

(no "Site" information available for 2VGM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr A:179 -Asp A:180

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VGM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VGM)

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YNL001W1YNL001W.1XIV:627459-6286191161DOM34_YEAST1-3863861A:1-381 (gaps)381

(-) 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:354
 aligned with DOM34_YEAST | P33309 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:381
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380 
          DOM34_YEAST     1 MKVISLKKDSFNKGGAVITLLPEDKEDLFTVYQIVDKDDELIFKKKFTSKLDEAGKKKSTDLVKLKIKVISEDFDMKDEYLKYKGVTVTDESGASNVDIPVGKYLSFTLDYVYPFTIIKQNFNKFMQKLLNEACNIEYKSDTAAVVLQEGIAHVCLVTSSSTILKQKIEYSMPKKKRTTDVLKFDEKTEKFYKAIYSAMKKDLNFDKLKTIILCSPGFYAKILMDKIFQYAEEEHNKKILDNKGMFFIAHCSTGYLQGINEVLKNPLYASKLQDTKYSKEIMVMDEFLLHLNKDDDKAWYGEKEVVKAAEYGAISYLLLTDKVLHSDNIAQREEYLKLMDSVESNGGKALVLSTLHSLGEELDQLTGIACILKYPLPDLDE 381
               SCOP domains d2vgma1       A:1-135 Dom34                                                                                                            d2vgma2 A:136-277 Dom34                                                                                                                       d2vgma3 A:278-381 Dom34                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains eRF1_1-      2vgmA03 A:1-136                                                                                                            ----eRF1_2-2vgmA02 A:141-274                                                                                                              --eRF1_3-2vgmA01 A:277-376                                                                            ----- Pfam domains
         Sec.struct. author .eeeeee------..eeeeee..hhhhhhhhhh......eeeeee..------------...eeeeeeeeeeeee....eeeeeeee................eeeee......eeeee...hhhhhhhhhhhhhhhhhh.eeeeee....eeeeee....eeeeeee.---------........hhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhhhhhhhhhhh....eeee......hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhh..eeeeeeehhhhh....hhhhhhhhhhhhhhh...eeeee...hhhhhhhhh...eeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-381 (gaps) UniProt: 1-386 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                     Transcript 1
                 2vgm A   1 MKVISLK------GGAVITLLPEDKEDLFTVYQIVDKDDELIFKKKF------------TDLVKLKIKVISEDFDMKDEYLKYKGVTVTDESGASNVDIPVGKYLSFTLDYVYPFTIIKQNFNKFMQKLLNEACNIEYKSDTAAVVLQEGIAHVCLVTSSSTILKQKIE---------TDVLKFDEKTEKFYKAIYSAMKKDLNFDKLKTIILCSPGFYAKILMDKIFQYAEEEHNKKILDNKGMFFIAHCSTGYLQGINEVLKNPLYASKLQDTKYSKEIMVMDEFLLHLNKDDDKAWYGEKEVVKAAEYGAISYLLLTDKVLHSDNIAQREEYLKLMDSVESNGGKALVLSTLHSLGEELDQLTGIACILKYPLPDLDE 381
                                  |  -   |    20        30        40      |  -        60        70        80        90       100       110       120       130       140       150       160        |-       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380 
                                  7     14                               47           60                                                                                                          169       179                                                                                                                                                                                                          

   Legend:   → Mismatch (orange background)
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    → 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  (3, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2VGM)

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Clan: S11_L18p (67)

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DOM34_YEAST | P33309)
molecular function
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0004521    endoribonuclease activity    Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    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).
    GO:0043022    ribosome binding    Interacting selectively and non-covalently with any part of a ribosome.
biological process
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0071025    RNA surveillance    The set of processes involved in identifying and degrading defective or aberrant RNAs.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0051321    meiotic cell cycle    Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions.
    GO:0070651    nonfunctional rRNA decay    An rRNA catabolic process that results in the targeted detection and degradation of aberrant rRNAs contained within translationally defective ribosomes, thereby acting as a quality-control system.
    GO:0070966    nuclear-transcribed mRNA catabolic process, no-go decay    The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA with stalls in translation elongation.
    GO:0070481    nuclear-transcribed mRNA catabolic process, non-stop decay    The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA that is lacking a stop codon.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0045727    positive regulation of translation    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0006417    regulation of translation    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0032790    ribosome disassembly    The disaggregation of a ribosome into its constituent components; includes the dissociation of ribosomal subunits.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
    GO:1990533    Dom34-Hbs1 complex    A protein complex consisting of one subunit known as Dom34 or Pelota that has similarity to translation termination factor eRF1, and another subunit, Hbs1, that is a GTPase with similarity to translation termination factor eRF3. The Dom34-Hbs1 complex has a role in cotranslational mRNA quality control by promoting ribosomal subunit dissociation and peptidyl-tRNA release when translation is stalled, facilitating no-go decay and nonstop decay.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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    Thr A:179 - Asp A:180   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        DOM34_YEAST | P333092vgn 3izq 3j16 5m1j

(-) Related Entries Specified in the PDB File

2vgn STRUCTURE OF YEAST DOM34 : A PROTEIN RELATED TO TRANSLATION TERMINATION FACTOR ERF1 AND INVOLVED IN NO-GO DECAY.