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(-) Description

Title :  CRYSTAL STRUCTURE OF A/EIF2ALPHA-ADIM2P-RRNA COMPLEX FROM PYROCOCCUS HORIKOSHII OT3
 
Authors :  M. Tanokura, M. Z. Jia, K. Nagata
Date :  10 Feb 10  (Deposition) - 21 Apr 10  (Release) - 29 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Proteins-Rrna Complex, 16S Rrna, Rna-Binding, Rna Processing, Initiation Factor, Protein Biosynthesis, Translation-Rna Binding Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Z. Jia, S. Horita, K. Nagata, M. Tanokura
An Archaeal Dim2-Like Protein, Adim2P, Forms A Ternary Complex With A/Eif2 Alpha And The 3' End Fragment Of 16S Rrna
J. Mol. Biol. V. 398 774 2010
PubMed-ID: 20363226  |  Reference-DOI: 10.1016/J.JMB.2010.03.055

(-) Compounds

Molecule 1 - TRANSLATION INITIATION FACTOR 2 SUBUNIT ALPHA
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PH0961
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953
    Synonym: EIF-2-ALPHA, AIF2-ALPHA
 
Molecule 2 - PUTATIVE UNCHARACTERIZED PROTEIN PH1566
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PH1566
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953
    Synonym: ADIM2P
 
Molecule 3 - RNA (5'-R(*GP*GP*AP*UP*CP*AP*CP*CP*UP*CP*C)-3')
    Chains: C
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 3AEV)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1S1PS50126 S1 domain profile.IF2A_PYRHO12-83  1A:12-83

(-) Exons   (0, 0)

(no "Exon" information available for 3AEV)

(-) 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:168
 aligned with IF2A_PYRHO | O58655 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:168
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166        
           IF2A_PYRHO     7 EYPEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRVDPRKGHIDLSLRRVTQQQRKAKLQEFKRAQKAENLLRLAAEKLGKDFEAAWREVWVPLEEEWGEVYAAFEDAAKDGIEVLKGHVPDEWLPVLKEIVENYVEVP 174
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeeeeeee..eeeeee......eeeee.hhh......hhhhh.....eeeeeeeeee....eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----S1  PDB: A:12-83 UniProt: 12-83                                         ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3aev A   7 EYPEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRVDPRKGHIDLSLRRVTQQQRKAKLQEFKRAQKAENLLRLAAEKLGKDFEAAWREVWVPLEEEWGEVYAAFEDAAKDGIEVLKGHVPDEWLPVLKEIVENYVEVP 174
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166        


Chain B from PDB  Type:PROTEIN  Length:177
 aligned with O59282_PYRHO | O59282 from UniProtKB/TrEMBL  Length:219

    Alignment length:183
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205   
         O59282_PYRHO    26 DEWEEFFKQEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSETGEVWITSTKETEDPLAVWKARDIVLAIGRGFSPERAFRLLNEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSVYGKTVAIIGNPIQIEIAKTAIEKLARGSPHGSVYRYLERRKKDL 208
               SCOP domains d3aevb1 B:26-115 automated matches                                                        d3aevb2 B:116      -208 automated matches                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh..eeeee.hhhhhhhhhh..hhhhhhhhhhhh.eeee.....eeeee........hhhhhhhhhhhhhhh..hhhhhhhhhh...eeeeee.hhh.------hhhhhhhhhhh..hhhhhhhhhhhh.eeeee..eeeeeehhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3aev B  26 DEWEEFFKQEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSETGEVWITSTKETEDPLAVWKARDIVLAIGRGFSPERAFRLLNEGEYLEIINLTDII------ALPRVRGRIIGRKGRTRQIIEEMSGASVSVYGKTVAIIGNPIQIEIAKTAIEKLARGSPHGSVYRYLERRKKDL 208
                                    35        45        55        65        75        85        95       105       115       125  |    135       145       155       165       175       185       195       205   
                                                                                                                                128    135                                                                         


Chain C from PDB  Type:RNA  Length:11
                                           
                 3aev C   1 GGAUCACCUCC  11
                                    10
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (IF2A_PYRHO | O58655)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0003743    translation initiation factor activity    Functions in the initiation of ribosome-mediated translation of mRNA into a polypeptide.
biological process
    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.
    GO:0006413    translational initiation    The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.

Chain B   (O59282_PYRHO | O59282)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.

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  3aev
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  IF2A_PYRHO | O58655
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  O59282_PYRHO | O59282
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 Related Entries

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

UniProtKB/TrEMBL
        O59282_PYRHO | O59282: 2e3u

(-) Related Entries Specified in the PDB File

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