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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SGT2 N DOMAIN AND THE GET5 UBL DOMAIN COMPLEX
 
Authors :  J. -Y. Tung, Y. -C. Li, C. -D. Hsiao
Date :  29 Nov 12  (Deposition) - 02 Oct 13  (Release) - 16 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Chaperone-Signaling Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. -Y. Tung, Y. -C. Li, T. -W. Lin, C. -D. Hsiao
Structure Of The Sgt2 Dimerization Domain Complexed With The Get5 Ubl Domain Involved In The Targeting Of Tail- Anchored Membrane Proteins To The Endoplasmic Reticulum.
Acta Crystallogr. , Sect. D V. 69 2081 2013
PubMed-ID: 24100326  |  Reference-DOI: 10.1107/S0907444913019379

(-) Compounds

Molecule 1 - SMALL GLUTAMINE-RICH TETRATRICOPEPTIDE REPEAT- CONTAINING PROTEIN 2
    ChainsA, B, D, E
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System VectorPET15B
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL DOMAIN, RESIDUES 1-72
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymSGT/UBP, VIRAL PROTEIN U-BINDING PROTEIN
 
Molecule 2 - UBIQUITIN-LIKE PROTEIN MDY2
    ChainsC, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System VectorPET15B
    Expression System Vector TypePLASMID
    FragmentUBIQUITIN-LIKE DOMAIN, RESIDUES 71-151
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymGOLGI TO ER TRAFFIC PROTEIN 5, MATING-DEFICIENT PROTEIN 2, TRANSLATION MACHINERY-ASSOCIATED PROTEIN 24

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit ABCDEF

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 3ZDM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala C:83 -Pro C:84
2Ala F:83 -Pro F:84

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.MDY2_YEAST74-152
 
  2C:74-150
F:74-150

(-) Exons   (0, 0)

(no "Exon" information available for 3ZDM)

(-) 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:69
 aligned with SGT2_YEAST | Q12118 from UniProtKB/Swiss-Prot  Length:346

    Alignment length:69
                                    11        21        31        41        51        61         
           SGT2_YEAST     2 SASKEEIAALIVNYFSSIVEKKEISEDGADSLNVAMDCISEAFGFEREAVSGILGKSEFKGQHLADILN  70
               SCOP domains --------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                 3zdm A   2 SASKEEIAALIVNYFSSIVEKKEISEDGADSLNVAMDCISEAFGFEREAVSGILGKSEFKGQHLADILN  70
                                    11        21        31        41        51        61         

Chain B from PDB  Type:PROTEIN  Length:50
 aligned with SGT2_YEAST | Q12118 from UniProtKB/Swiss-Prot  Length:346

    Alignment length:50
                                    11        21        31        41        51
           SGT2_YEAST     2 SASKEEIAALIVNYFSSIVEKKEISEDGADSLNVAMDCISEAFGFEREAV  51
               SCOP domains -------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------- Transcript
                 3zdm B   2 SASKEEIAALIVNYFSSIVEKKEISEDGADSLNVAMDCISEAFGFEREAV  51
                                    11        21        31        41        51

Chain C from PDB  Type:PROTEIN  Length:79
 aligned with MDY2_YEAST | Q12285 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:79
                                    81        91       101       111       121       131       141         
           MDY2_YEAST    72 AAVHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKASHISEIKLLLKGKVLHDNLFLSDLKVTPANSTITVMIKP 150
               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: C:74-150 UniProt: 74-152                                    PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                 3zdm C  72 AAVHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKASHISEIKLLLKGKVLHDNLFLSDLKVTPANSTITVMIKP 150
                                    81        91       101       111       121       131       141         

Chain D from PDB  Type:PROTEIN  Length:69
 aligned with SGT2_YEAST | Q12118 from UniProtKB/Swiss-Prot  Length:346

    Alignment length:69
                                    11        21        31        41        51        61         
           SGT2_YEAST     2 SASKEEIAALIVNYFSSIVEKKEISEDGADSLNVAMDCISEAFGFEREAVSGILGKSEFKGQHLADILN  70
               SCOP domains --------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                 3zdm D   2 SASKEEIAALIVNYFSSIVEKKEISEDGADSLNVAMDCISEAFGFEREAVSGILGKSEFKGQHLADILN  70
                                    11        21        31        41        51        61         

Chain E from PDB  Type:PROTEIN  Length:50
 aligned with SGT2_YEAST | Q12118 from UniProtKB/Swiss-Prot  Length:346

    Alignment length:50
                                    11        21        31        41        51
           SGT2_YEAST     2 SASKEEIAALIVNYFSSIVEKKEISEDGADSLNVAMDCISEAFGFEREAV  51
               SCOP domains -------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------- Transcript
                 3zdm E   2 SASKEEIAALIVNYFSSIVEKKEISEDGADSLNVAMDCISEAFGFEREAV  51
                                    11        21        31        41        51

Chain F from PDB  Type:PROTEIN  Length:79
 aligned with MDY2_YEAST | Q12285 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:79
                                    81        91       101       111       121       131       141         
           MDY2_YEAST    72 AAVHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKASHISEIKLLLKGKVLHDNLFLSDLKVTPANSTITVMIKP 150
               SCOP domains ------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....eeeeeee....hhhhhhhhhhhh....hhh.eeeee..ee......hhhhh......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --UBIQUITIN_2  PDB: F:74-150 UniProt: 74-152                                    PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                 3zdm F  72 AAVHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKASHISEIKLLLKGKVLHDNLFLSDLKVTPANSTITVMIKP 150
                                    81        91       101       111       121       131       141         

   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 3ZDM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,D,E   (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.

Chain C,F   (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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    Ala C:83 - Pro C:84   [ RasMol ]  
    Ala F:83 - Pro F:84   [ RasMol ]  
 

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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 3vej 4a20 4asw 4goc 4pwx 5bw8 5bwk
        SGT2_YEAST | Q121182lxb 2lxc 4asv 4asw

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3ZDM)