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(-) Description

Title :  CRYSTAL STRUCTURE OF M.JANNASCHII EIF6
 
Authors :  C. M. Groft, R. Beckmann, A. Sali, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  02 Nov 00  (Deposition) - 22 Nov 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Alpha-Beta-Barrel Velcro Closure Subdomain, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. M. Groft, R. Beckmann, A. Sali, S. K. Burley
Crystal Structures Of Ribosome Anti-Association Factor If6.
Nat. Struct. Biol. V. 7 1156 2000
PubMed-ID: 11101899  |  Reference-DOI: 10.1038/82017
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSLATION INITIATION FACTOR 6
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET28A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: MJ0048
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190
    Synonym: EIF-6

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1G61)

(-) Sites  (0, 0)

(no "Site" information available for 1G61)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1G61)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1G61)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1G61)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1G61)

(-) Exons   (0, 0)

(no "Exon" information available for 1G61)

(-) 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:225
 aligned with IF6_METJA | Q60357 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:225
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222     
           IF6_METJA      3 MIIRKYFSGIPTIGVLALTTEEITLLPIFLDKDDVNEVSEVLETKCLQTNIGGSSLVGSLSVANKYGLLLPKIVEDEELDRIKNFLKENNLDLNVEIIKSKNTALGNLILTNDKGALISPELKDFKKDIEDSLNVEVEIGTIAELPTVGSNAVVTNKGCLTHPLVEDDELEFLKSLFKVEYIGKGTANKGTTSVGACIIANSKGAVVGGDTTGPELLIIEDALGL  227
               SCOP domains d1g61a_ A: Ribosome anti-association factor eIF6 (aIF6)                                                                                                                                                                           SCOP domains
               CATH domains 1g61A00 A:2003-2227 L-arginine/glycine Amidinotransferase; Chain A                                                                                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......hhhhhhee...eeee....hhhhhhhhhhhhh.eeee.......hhhhhhee...eeeee...hhhhhhhhhhhhhhh....eeeee.....hhhhheee...eeee.hhhhhhhhhhhhhhh.eeee............eee...eeee....hhhhhhhhhhhhh..eeee........hhhh.eee....eeee...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1g61 A 2003 MIIRKYFSGIPTIGVLALTTEEITLLPIFLDKDDVNEVSEVLETKCLQTNIGGSSLVGSLSVANKYGLLLPKIVEDEELDRIKNFLKENNLDLNVEIIKSKNTALGNLILTNDKGALISPELKDFKKDIEDSLNVEVEIGTIAELPTVGSNAVVTNKGCLTHPLVEDDELEFLKSLFKVEYIGKGTANKGTTSVGACIIANSKGAVVGGDTTGPELLIIEDALGL 2227
                                  2012      2022      2032      2042      2052      2062      2072      2082      2092      2102      2112      2122      2132      2142      2152      2162      2172      2182      2192      2202      2212      2222     


Chain B from PDB  Type:PROTEIN  Length:225
 aligned with IF6_METJA | Q60357 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:225
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222     
           IF6_METJA      3 MIIRKYFSGIPTIGVLALTTEEITLLPIFLDKDDVNEVSEVLETKCLQTNIGGSSLVGSLSVANKYGLLLPKIVEDEELDRIKNFLKENNLDLNVEIIKSKNTALGNLILTNDKGALISPELKDFKKDIEDSLNVEVEIGTIAELPTVGSNAVVTNKGCLTHPLVEDDELEFLKSLFKVEYIGKGTANKGTTSVGACIIANSKGAVVGGDTTGPELLIIEDALGL  227
               SCOP domains d1g61b_ B: Ribosome anti-association factor eIF6 (aIF6)                                                                                                                                                                           SCOP domains
               CATH domains 1g61B00 B:4003-4227 L-arginine/glycine Amidinotransferase; Chain A                                                                                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......hhhhhhee...eeee....hhhhhhhhhhhhh.eeee.......hhhhhhee...eeeee...hhhhhhhhhhhhhhh....eeeee.....hhhhheee...eeee.hhhhhhhhhhhhhhh.eeee............eee...eeee....hhhhhhhhhhhhh..eeee........hhhh.eee....eeee...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1g61 B 4003 MIIRKYFSGIPTIGVLALTTEEITLLPIFLDKDDVNEVSEVLETKCLQTNIGGSSLVGSLSVANKYGLLLPKIVEDEELDRIKNFLKENNLDLNVEIIKSKNTALGNLILTNDKGALISPELKDFKKDIEDSLNVEVEIGTIAELPTVGSNAVVTNKGCLTHPLVEDDELEFLKSLFKVEYIGKGTANKGTTSVGACIIANSKGAVVGGDTTGPELLIIEDALGL 4227
                                  4012      4022      4032      4042      4052      4062      4072      4082      4092      4102      4112      4122      4132      4142      4152      4162      4172      4182      4192      4202      4212      4222
   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  (1, 2)

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

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1G61)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (IF6_METJA | Q60357)
molecular function
    GO:0043023    ribosomal large subunit binding    Interacting selectively and non-covalently with any part of the larger ribosomal subunit.
    GO:0043022    ribosome binding    Interacting selectively and non-covalently with any part of a ribosome.
    GO:0003743    translation initiation factor activity    Functions in the initiation of ribosome-mediated translation of mRNA into a polypeptide.
biological process
    GO:1902626    assembly of large subunit precursor of preribosome    The aggregation, arrangement and bonding together of a set of components to form the large subunit precursor of the preribosome.
    GO:0000460    maturation of 5.8S rRNA    Any process involved in the maturation of a precursor 5.8S ribosomal RNA (rRNA) molecule into a mature 5.8S rRNA molecule.
    GO:0000470    maturation of LSU-rRNA    Any process involved in the maturation of a precursor Large SubUnit (LSU) ribosomal RNA (rRNA) molecule into a mature LSU-rRNA molecule.
    GO:0042256    mature ribosome assembly    The aggregation, arrangement and bonding together of the large and small ribosomal subunits into a functional ribosome.
    GO:0000054    ribosomal subunit export from nucleus    The directed movement of a ribosomal subunit from the nucleus into the cytoplasm.
    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.
cellular component
    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:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0030687    preribosome, large subunit precursor    A preribosomal complex consisting of 27SA, 27SB, and/or 7S pre-rRNA, 5S rRNA, ribosomal proteins including late-associating large subunit proteins, and associated proteins; a precursor of the eukaryotic cytoplasmic large ribosomal subunit.

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  1g61
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  IF6_METJA | Q60357
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 Related Entries

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

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(-) Related Entries Specified in the PDB File

1g62 S.CEREVISIAE EIF6 RELATED ID: NYSGXRC-P111A RELATED DB: TARGETDB