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(-) Description

Title :  CRYSTAL STRUCTURE OF THE UBL DOMAIN OF MDY2 (GET5) AT 1.78A
 
Authors :  A. C. Simon, P. J. Simpson, J. W. Murray, R. L. Isaacson
Date :  21 Sep 11  (Deposition) - 14 Nov 12  (Release) - 13 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Protein Binding, Get-Pathway, Tail-Anchored Proteins (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. C. Simon, P. J. Simpson, R. M. Goldstone, E. M. Krysztofinska, J. W. Murray, S. High, R. L. Isaacson
Structure Of The Sgt2/Get5 Complex Provides Insights Into Get-Mediated Targeting Of Tail-Anchored Membrane Proteins
Proc. Natl. Acad. Sci. Usa V. 110 1327 2013
PubMed-ID: 23297211  |  Reference-DOI: 10.1073/PNAS.1207518110

(-) Compounds

Molecule 1 - UBIQUITIN-LIKE PROTEIN MDY2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET46
    Expression System Vector TypePLASMID
    FragmentGET5 UBL-LIKE DOMAIN, RESIDUES 70-152
    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

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:127 , ASP A:128 , HOH A:2025BINDING SITE FOR RESIDUE SO4 A1152
2AC2SOFTWAREGLN A:82 , ALA A:83BINDING SITE FOR RESIDUE SO4 A1153
3AC3SOFTWARELYS A:124 , VAL A:125 , HOH A:2033 , HOH A:2037BINDING SITE FOR RESIDUE SO4 A1154

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4A20)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala A:83 -Pro A:84

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4A20)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.MDY2_YEAST74-152  1A:74-151
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.MDY2_YEAST74-152  2A:74-151

(-) Exons   (0, 0)

(no "Exon" information available for 4A20)

(-) 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:80
 aligned with MDY2_YEAST | Q12285 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:80
                                    81        91       101       111       121       131       141       151
           MDY2_YEAST    72 AAVHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKASHISEIKLLLKGKVLHDNLFLSDLKVTPANSTITVMIKPN 151
               SCOP domains -------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....eeeeeee....hhhhhhhhhhhh....hhh.eeeee..eee.....hhhh.......eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --UBIQUITIN_2  PDB: A:74-151 UniProt: 74-152                                     PROSITE
                 Transcript -------------------------------------------------------------------------------- Transcript
                 4a20 A  72 AAVHLTLKKIQAPKFSIEHDFSPSDTILQIKQHLISEEKASHISEIKLLLKGKVLHDNLFLSDLKVTPANSTITVMIKPN 151
                                    81        91       101       111       121       131       141       151

   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 4A20)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4A20)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4A20)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(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.

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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 3zdm 4asw 4goc 4pwx 5bw8 5bwk

(-) Related Entries Specified in the PDB File

2wpv CRYSTAL STRUCTURE OF S. CEREVISIAE GET4-GET5 COMPLEX