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(-) Description

Title :  C-TERMINAL DOMAIN OF ELONGATION FACTOR SELB COMPLEXED WITH SECIS RNA
 
Authors :  S. Yoshizawa, L. Rasubala, T. Ose, D. Kohda, D. Fourmy, K. Maenaka
Date :  11 Nov 04  (Deposition) - 25 Jan 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G
Keywords :  Winged-Helix, Translation/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Yoshizawa, L. Rasubala, T. Ose, D. Kohda, D. Fourmy, K. Maenaka
Structural Basis For Mrna Recognition By Elongation Factor Selb
Nat. Struct. Mol. Biol. V. 12 198 2005
PubMed-ID: 15665870  |  Reference-DOI: 10.1038/NSMB890
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'- R(*GP*GP*CP*GP*UP*UP*GP*CP*CP*GP*GP*UP*CP*U*GP*GP*CP*AP*AP* CP*GP*CP*C)-3'
    Chains: E, F, G
    Engineered: YES
    Other Details: SELENOCYSTEIN INCORPORATED SEQUENCE OF RNA. THE FIRST 3 AND LAST 3 RESIDUES ARE CLONING ARTIFACTS.
    Synonym: SECIS RNA
    Synthetic: YES
 
Molecule 2 - SELENOCYSTEINE-SPECIFIC ELONGATION FACTOR
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PGEX-2T
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: SECIS BINDING DOMAIN
    Gene: SELB
    Organism Scientific: MOORELLA THERMOACETICA
    Organism Taxid: 1525
    Synonym: SELB TRANSLATION FACTOR

 Structural Features

(-) Chains, Units

  1234567
Asymmetric/Biological Unit : ABCDEFG

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1WSU)

(-) Sites  (0, 0)

(no "Site" information available for 1WSU)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WSU)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WSU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WSU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WSU)

(-) Exons   (0, 0)

(no "Exon" information available for 1WSU)

(-) 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:124
 aligned with SELB_MOOTH | Q46455 from UniProtKB/Swiss-Prot  Length:634

    Alignment length:142
                                   502       512       522       532       542       552       562       572       582       592       602       612       622       632  
           SELB_MOOTH   493 GRLQLAANTVALAGFTPSFSETQKKLLKDLEDKYRVSRWQPPSFKEVAGSFNLDPSELEELLHYLVREGVLVKINDEFYWHRQALGEAREVIKNLASTGPFGLAEARDALGSSRKYVLPLLEYLDQVKFTRRVGDKRVVVGN 634
               SCOP domains -------------------d1wsua1 A:512-574 C-terminal fragment of elongation factor SelBd1wsua2 A:575-634                                            SCOP domains
               CATH domains 1                  wsuA01 A:511-573 'winged helix' repressor DNA binding domain  1wsuA02 A:574-634 'winged helix' repressor DNA binding domain CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .------------------..hhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhh..eee.....eeehhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wsu A 511 G------------------SETQKKLLKDLEDKYRVSRWQPPSFKEVAGSFNLDPSELEELLHYLVREGVLVKINDEFYWHRQALGEAREVIKNLASTGPFGLAEARDALGSSRKYVLPLLEYLDQVKFTRRVGDKRVVVGN 634
                            |        -       512       522       532       542       552       562       572       582       592       602       612       622       632  
                            |                512                                                                                                                          
                          511                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:122
 aligned with SELB_MOOTH | Q46455 from UniProtKB/Swiss-Prot  Length:634

    Alignment length:140
                                   502       512       522       532       542       552       562       572       582       592       602       612       622       632
           SELB_MOOTH   493 GRLQLAANTVALAGFTPSFSETQKKLLKDLEDKYRVSRWQPPSFKEVAGSFNLDPSELEELLHYLVREGVLVKINDEFYWHRQALGEAREVIKNLASTGPFGLAEARDALGSSRKYVLPLLEYLDQVKFTRRVGDKRVVV 632
               SCOP domains -------------------d1wsub1 B:512-574 C-terminal fragment of elongation factor SelBd1wsub2 B:575-632                                          SCOP domains
               CATH domains 1                  wsuB01 B:511-573 'winged helix' repressor DNA binding domain  1wsuB02 B:574-632                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author h------------------hhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhh..eee.....eeehhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wsu B 511 G------------------SETQKKLLKDLEDKYRVSRWQPPSFKEVAGSFNLDPSELEELLHYLVREGVLVKINDEFYWHRQALGEAREVIKNLASTGPFGLAEARDALGSSRKYVLPLLEYLDQVKFTRRVGDKRVVV 632
                            |        -       512       522       532       542       552       562       572       582       592       602       612       622       632
                          511                512                                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:102
 aligned with SELB_MOOTH | Q46455 from UniProtKB/Swiss-Prot  Length:634

    Alignment length:116
                                   526       536       546       556       566       576       586       596       606       616       626      
           SELB_MOOTH   517 KLLKDLEDKYRVSRWQPPSFKEVAGSFNLDPSELEELLHYLVREGVLVKINDEFYWHRQALGEAREVIKNLASTGPFGLAEARDALGSSRKYVLPLLEYLDQVKFTRRVGDKRVVV 632
               SCOP domains d1wsuc1 C:517-574                                         d1wsuc2 C:575-632                                          SCOP domains
               CATH domains ------------------------          -----------------------1wsuC02 C:574-632                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh....hhhhhh----------..hhhhhhhh..eee.....eeehhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhh..ee----..ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 1wsu C 517 KLLKDLEDKYRVSRWQPPSFKEVA----------EELLHYLVREGVLVKINDEFYWHRQALGEAREVIKNLASTGPFGLAEARDALGSSRKYVLPLLEYLDQVKFTR----KRVVV 632
                                   526       536   |     -    |  556       566       576       586       596       606       616      |  - |    
                                                 540        551                                                                     623  628    


Chain D from PDB  Type:PROTEIN  Length:121
 aligned with SELB_MOOTH | Q46455 from UniProtKB/Swiss-Prot  Length:634

    Alignment length:123
                                   521       531       541       551       561       571       581       591       601       611       621       631   
           SELB_MOOTH   512 SETQKKLLKDLEDKYRVSRWQPPSFKEVAGSFNLDPSELEELLHYLVREGVLVKINDEFYWHRQALGEAREVIKNLASTGPFGLAEARDALGSSRKYVLPLLEYLDQVKFTRRVGDKRVVVGN 634
               SCOP domains d1wsud1 D:512-574 C-terminal fragment of elongation factor SelBd1wsud2 D:575-  634                                          SCOP domains
               CATH domains 1wsuD01 D:512-573 'winged helix' repressor DNA binding domain 1wsuD02 D:574-6  34 'winged helix' repressor DNA binding doma CATH domains
           Pfam domains (1) ---------------------------------------------------------------------SelB-win  g_3-1wsuD01 D:581-632                     -- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------SelB-win  g_3-1wsuD02 D:581-632                     -- Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------SelB-win  g_3-1wsuD03 D:581-632                     -- Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------SelB-win  g_3-1wsuD04 D:581-632                     -- Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhh..eee.....eeehhhhhhhhhhhhhh.--...hhhhhhhhh..hhhhhhhhhhhhhhh..ee......ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wsu D 512 SETQKKLLKDLEDKYRVSRWQPPSFKEVAGSFNLDPSELEELLHYLVREGVLVKINDEFYWHRQALGEAREVIKNLA--GPFGLAEARDALGSSRKYVLPLLEYLDQVKFTRRVGDKRVVVGN 634
                                   521       531       541       551       561       571       581      |591       601       611       621       631   
                                                                                                      588  |                                           
                                                                                                         591                                           


Chain E from PDB  Type:RNA  Length:22
                                                      
                 1wsu E  13 GGCGUUGCCGGUCGGCAACGCC  35
                                    22  ||    33  
                                       25|        
                                        27        


Chain F from PDB  Type:RNA  Length:22
                                                      
                 1wsu F  13 GGCGUUGCCGGUCGGCAACGCC  35
                                    22  ||    33  
                                       25|        
                                        27        


Chain G from PDB  Type:RNA  Length:21
                                                     
                 1wsu G  13 GGCGUUGCCGGUGGCAACGCC  35
                                    22 ||     34 
                                      24|        
                                       27
   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  (1, 8)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 7)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: SelB-wing_3] (4)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (SELB_MOOTH | Q46455)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0003746    translation elongation factor activity    Functions in chain elongation during polypeptide synthesis at the ribosome.
biological process
    GO:0001514    selenocysteine incorporation    The incorporation of selenocysteine into a peptide; uses a special tRNA that recognizes the UGA codon as selenocysteine, rather than as a termination codon. Selenocysteine is synthesized from serine before its incorporation; it is not a posttranslational modification of peptidyl-cysteine.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  1wsu
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 Related Entries

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

UniProtKB/Swiss-Prot
        SELB_MOOTH | Q46455: 1lva 2ply 2uwm 2v9v

(-) Related Entries Specified in the PDB File

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