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(-) Description

Title :  CRYSTAL STRUCTURE OF THE GET5 CARBOXYL DOMAIN FROM S. CEREVISIAE
 
Authors :  J. W. Chartron, D. G. Vandervelde, M. Rao, W. M. Clemons Jr.
Date :  08 Jan 12  (Deposition) - 25 Jan 12  (Release) - 28 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.23
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha Helical, Dimerization, Homodimerization, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. W. Chartron, D. G. Vandervelde, M. Rao, W. M. Clemons
Get5 Carboxyl-Terminal Domain Is A Novel Dimerization Motif That Tethers An Extended Get4/Get5 Complex.
J. Biol. Chem. V. 287 8310 2012
PubMed-ID: 22262836  |  Reference-DOI: 10.1074/JBC.M111.333252

(-) Compounds

Molecule 1 - UBIQUITIN-LIKE PROTEIN MDY2
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-33B
    Expression System StrainBL21(DE3)STAR
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentCARBOXYL DOMAIN RESIDUES 175-212
    GeneGET5, MDY2, TMA24, YOL111C
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid559292
    StrainATCC 204508 / S288C
    SynonymGOLGI TO ER TRAFFIC PROTEIN 5, MATING-DEFICIENT PROTEIN 2, TRANSLATION MACHINERY-ASSOCIATED PROTEIN 24

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:203 , HOH A:331 , ARG B:203 , LYS B:212 , HOH B:433 , HOH B:434BINDING SITE FOR RESIDUE PO4 B 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3VEJ)

(-) 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
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Chain A from PDB  Type:PROTEIN  Length:40
 aligned with MDY2_YEAST | Q12285 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:40
                                   182       192       202       212
           MDY2_YEAST   173 QELTVPWDDIEALLKNNFENDQAAVRQVMERLQKGWSLAK 212
               SCOP domains ---------------------------------------- SCOP domains
               CATH domains ---------------------------------------- CATH domains
               Pfam domains ---------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------- PROSITE
                 Transcript ---------------------------------------- Transcript
                 3vej A 173 VDLTVPWDDIEALLKNNFENDQAAVRQVMERLQKGWSLAK 212
                                   182       192       202       212

Chain B from PDB  Type:PROTEIN  Length:41
 aligned with MDY2_YEAST | Q12285 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:41
                                   181       191       201       211 
           MDY2_YEAST   172 PQELTVPWDDIEALLKNNFENDQAAVRQVMERLQKGWSLAK 212
               SCOP domains ----------------------------------------- SCOP domains
               CATH domains ----------------------------------------- CATH domains
               Pfam domains ----------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------- PROSITE
                 Transcript ----------------------------------------- Transcript
                 3vej B 172 SVDLTVPWDDIEALLKNNFENDQAAVRQVMERLQKGWSLAK 212
                                   181       191       201       211 

   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MDY2_YEAST | Q12285)
molecular function
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    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:0000753    cell morphogenesis involved in conjugation with cellular fusion    The change in form (cell shape and size) that occurs during sexual reproduction in order to facilitate direct contact between the compatible mating types in organisms that undergo conjugation cellular fusion.
    GO:0006620    posttranslational protein targeting to endoplasmic reticulum membrane    The targeting of proteins to a membrane that occurs after their translation. Some secretory proteins exhibit posttranslational transport into the endoplasmic reticulum (ER) lumen: they are synthesized in their entirety on free cytosolic ribosomes and then released into the cytosol, where they are bound by chaperones which keep them in an unfolded state, and subsequently are translocated across the ER membrane.
    GO:0045048    protein insertion into ER membrane    The process that results in incorporation of a protein into an endoplasmic reticulum (ER) membrane. It depends on specific topogenic sequences of amino acids that ensure that a protein acquires the proper orientation during its insertion into the ER membrane.
cellular component
    GO:0072380    TRC complex    An ER membrane insertion complex that contains subunits that recognize two types of transmembrane domain signals. In budding yeast the complex contains Get4p, Get5p, Sgt2p, and at least two heat shock proteins (HSPs).
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0010494    cytoplasmic stress granule    A dense aggregation in the cytosol composed of proteins and RNAs that appear when the cell is under stress.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005840    ribosome    An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MDY2_YEAST | Q122852lnz 2lxa 2lxc 2wpv 3lku 3zdm 4a20 4asw 4goc 4pwx 5bw8 5bwk

(-) Related Entries Specified in the PDB File

2lnz SOLUTION STRUCTURE OF THE S. CEREVISIAE HOMOLOG
2lo0