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(-) Description

Title :  SOLUTION STRUCTURE OF THE COMPLEX BETWEEN THE SGT2 HOMODIMERIZATION DOMAIN AND THE GET5 UBL DOMAIN
 
Authors :  J. W. Chartron, D. G. Vandervelde, W. M. Clemons Jr.
Date :  19 Aug 12  (Deposition) - 21 Nov 12  (Release) - 16 Jan 13  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C  (10x)
NMR Structure *:  A,B,C  (1x)
Keywords :  Ubiquitin-Like Domain, Protein-Protein Interaction, Four-Helix Bundle, Get Pathway, Protein Binding-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. W. Chartron, D. G. Vandervelde, W. M. Clemons
Structures Of The Sgt2/Sgta Dimerization Domain With The Get5/Ubl4A Ubl Domain Reveal An Interaction That Forms A Conserved Dynamic Interface.
Cell Rep V. 2 1620 2012
PubMed-ID: 23142665  |  Reference-DOI: 10.1016/J.CELREP.2012.10.010

(-) Compounds

Molecule 1 - UBIQUITIN-LIKE PROTEIN MDY2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET33B
    Expression System StrainNICO21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUBIQUITIN-LIKE DOMAIN
    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
 
Molecule 2 - SMALL GLUTAMINE-RICH TETRATRICOPEPTIDE REPEAT-CONTAINING PROTEIN 2
    ChainsB, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET33B
    Expression System StrainNICO21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL DOMAIN
    GeneSGT2, UNF346, YOR007C
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid559292
    StrainATCC 204508 / S288C
    SynonymSGT/UBP, VIRAL PROTEIN U-BINDING PROTEIN

 Structural Features

(-) Chains, Units

  123
NMR Structure (10x)ABC
NMR Structure * (1x)ABC

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2LXC)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 10)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10Ala A:83 -Pro A:84

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.MDY2_YEAST74-152  1A:74-151
NMR Structure * (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.MDY2_YEAST74-152  1A:74-151

(-) Exons   (0, 0)

(no "Exon" information available for 2LXC)

(-) Sequences/Alignments

NMR Structure
   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:81
 aligned with MDY2_YEAST | Q12285 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:111
                                    82        92       102       112       122       132       142       152       162       172       182 
           MDY2_YEAST    73 AVHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKASHISEIKLLLKGKVLHDNLFLSDLKVTPANSTITVMIKPNPTISKEPEAEKSTNSPAPAPPQELTVPWDDIE 183
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....eeeeeee....hhhhhhhhhhhh....hhh.eeeee..ee.....hhhhhh......eeeeee...------------------------------.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -UBIQUITIN_2  PDB: A:74-151 UniProt: 74-152                                     ------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 2lxc A  73 MVHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKASHISEIKLLLKGKVLHDNLFLSDLKVTPANSTITVMIKPN------------------------------LE 153
                                    82        92       102       112       122       132       142        |-         -         -       152 
                                                                                                        151                            152 

Chain B from PDB  Type:PROTEIN  Length:74
 aligned with SGT2_YEAST | Q12118 from UniProtKB/Swiss-Prot  Length:346

    Alignment length:74
                              1                                                                       
                              |      8        18        28        38        48        58        68    
           SGT2_YEAST     - --MSASKEEIAALIVNYFSSIVEKKEISEDGADSLNVAMDCISEAFGFEREAVSGILGKSEFKGQHLADILNSA  72
               SCOP domains -------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 2lxc B  -1 SVDSASKEEIAALIVNYFSSIVEKKEISEDGADSLNVAMDCISEAFGFEREAVSGILGKSEFKGQHLADILNSA  72
                                     8        18        28        38        48        58        68    

Chain C from PDB  Type:PROTEIN  Length:74
 aligned with SGT2_YEAST | Q12118 from UniProtKB/Swiss-Prot  Length:346

    Alignment length:74
                              1                                                                       
                              |      8        18        28        38        48        58        68    
           SGT2_YEAST     - --MSASKEEIAALIVNYFSSIVEKKEISEDGADSLNVAMDCISEAFGFEREAVSGILGKSEFKGQHLADILNSA  72
               SCOP domains -------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 2lxc C  -1 SVDSASKEEIAALIVNYFSSIVEKKEISEDGADSLNVAMDCISEAFGFEREAVSGILGKSEFKGQHLADILNSA  72
                                     8        18        28        38        48        58        68    

   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  (0, 0)

(no "SCOP Domain" information available for 2LXC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2LXC)

(-) Gene Ontology  (13, 17)

NMR Structure(hide GO term definitions)
Chain A   (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.

Chain B,C   (SGT2_YEAST | Q12118)
molecular function
    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:0032947    protein complex scaffold activity    A structural molecule activity that provides a physical support for the assembly of a multiprotein complex. The scaffold may or may not be part of the final complex.
biological process
    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:0009408    response to heat    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 heat stimulus, a temperature stimulus above the optimal temperature for that organism.
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.

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    Ala A:83 - Pro A:84   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        MDY2_YEAST | Q122852lnz 2lxa 2wpv 3lku 3vej 3zdm 4a20 4asw 4goc 4pwx 5bw8 5bwk
        SGT2_YEAST | Q121182lxb 3zdm 4asv 4asw

(-) Related Entries Specified in the PDB File

2lxa SOLUTION STRUCTURE OF GET5 UBIQUITIN LIKE DOMAIN
2lxb SOLUTION STRUCTURE OF SGT2 HOMODIMERIZATION DOMAIN
4goc CRYSTAL STRUCTURE OF GET5 UBIQUITIN LIKE DOMAIN
4god CRYSTAL STRUCTURE OF SGTA HOMODIMERIZATION DOMAIN, THE HUMAN HOMOLOG
4goe CRYSTAL STRUCTURE OF SGTA HOMODIMERIZATION DOMAIN, THE HUMAN HOMOLOG
4gof CRYSTAL STRUCTURE OF SGTA HOMODIMERIZATION DOMAIN, THE HUMAN HOMOLOG RELATED ID: 18671 RELATED DB: BMRB