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(-) Description

Title :  CRYSTAL STRUCTURE OF A HEPTAMERIC SM-LIKE PROTEIN FROM METHANOBACTERIUM THERMOAUTOTROPHICUM
 
Authors :  B. M. Collins, N. Naidoo, S. J. Harrop, P. M. G. Curmi, B. C. Mabbutt
Date :  16 Aug 02  (Deposition) - 11 Dec 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G
Keywords :  Lsm, Rna-Binding, Archea, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. M. Collins, N. Naidoo, S. J. Harrop, P. M. G. Curmi, B. C. Mabbutt
Refined Structure Of Sm-Like Protein Heptamer From Methanobacterium Thermoautotrophicum
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SM-LIKE PROTEIN
    ChainsA, B, C, D, E, F, G
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPGEX-4T-2
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    GeneMT0649
    Organism ScientificMETHANOTHERMOBACTER THERMAUTOTROPHICUS
    Organism Taxid145262
    SynonymSNRNP SM-LIKE PROTEIN

 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 1MGQ)

(-) Sites  (0, 0)

(no "Site" information available for 1MGQ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1MGQ)

(-) 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:74
 aligned with RUXX_METTH | O26745 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:74
                                    17        27        37        47        57        67        77    
            RUXX_METTH    8 RVNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISP 81
               SCOP domains d1mgqa_ A: Archaeal homoheptameric Sm protein                              SCOP domains
               CATH domains 1mgqA00 A:8-81  [code=2.30.30.100, no name defined]                        CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhh...eeeeee...eeeeeeeeee.....eeeeeeeeee..eeeeeeeeeee....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                  1mgq A  8 RVNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISP 81
                                    17        27        37        47        57        67        77    

Chain B from PDB  Type:PROTEIN  Length:74
 aligned with RUXX_METTH | O26745 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:74
                                    17        27        37        47        57        67        77    
            RUXX_METTH    8 RVNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISP 81
               SCOP domains d1mgqb_ B: Archaeal homoheptameric Sm protein                              SCOP domains
               CATH domains 1mgqB00 B:8-81  [code=2.30.30.100, no name defined]                        CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhh....eeeeee....eeeeeeeee.....eeeeeeeee....eeeeeeeeee....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                  1mgq B  8 RVNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISP 81
                                    17        27        37        47        57        67        77    

Chain C from PDB  Type:PROTEIN  Length:74
 aligned with RUXX_METTH | O26745 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:74
                                    17        27        37        47        57        67        77    
            RUXX_METTH    8 RVNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISP 81
               SCOP domains d1mgqc_ C: Archaeal homoheptameric Sm protein                              SCOP domains
               CATH domains 1mgqC00 C:8-81  [code=2.30.30.100, no name defined]                        CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhh...eeeeee...eeeeeeeeee.....eeeeeeeeee..eeeeeeeeeee....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                  1mgq C  8 RVNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISP 81
                                    17        27        37        47        57        67        77    

Chain D from PDB  Type:PROTEIN  Length:73
 aligned with RUXX_METTH | O26745 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:73
                                    18        28        38        48        58        68        78   
            RUXX_METTH    9 VNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISP 81
               SCOP domains d1mgqd_ D: Archaeal homoheptameric Sm protein                             SCOP domains
               CATH domains 1mgqD00 D:9-81  [code=2.30.30.100, no name defined]                       CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhh...eeeeee....eeeeeeeee.....eeeeeeeeee..eeeeeeeeeee....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                  1mgq D  9 VNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISP 81
                                    18        28        38        48        58        68        78   

Chain E from PDB  Type:PROTEIN  Length:73
 aligned with RUXX_METTH | O26745 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:73
                                    18        28        38        48        58        68        78   
            RUXX_METTH    9 VNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISP 81
               SCOP domains d1mgqe_ E: Archaeal homoheptameric Sm protein                             SCOP domains
               CATH domains 1mgqE00 E:9-81  [code=2.30.30.100, no name defined]                       CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhh....eeeeee...eeeeeeeeee.....eeeeeeeeee..eeeeeeeeeee....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                  1mgq E  9 VNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISP 81
                                    18        28        38        48        58        68        78   

Chain F from PDB  Type:PROTEIN  Length:70
 aligned with RUXX_METTH | O26745 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:70
                                    21        31        41        51        61        71        81
            RUXX_METTH   12 QRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISP 81
               SCOP domains d1mgqf_ F: Archaeal homoheptameric Sm protein                          SCOP domains
               CATH domains 1mgqF00 F:12-81  [code=2.30.30.100, no name defined]                   CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh...eeeeee....eeeeeeeee.....eeeeeeeeee..eeeeeeeeeee....eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                  1mgq F 12 QRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISP 81
                                    21        31        41        51        61        71        81

Chain G from PDB  Type:PROTEIN  Length:73
 aligned with RUXX_METTH | O26745 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:73
                                    18        28        38        48        58        68        78   
            RUXX_METTH    9 VNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISP 81
               SCOP domains d1mgqg_ G: Archaeal homoheptameric Sm protein                             SCOP domains
               CATH domains 1mgqG00 G:9-81  [code=2.30.30.100, no name defined]                       CATH domains
           Pfam domains (1) -------LSM-1mgqG01 G:16-81                                                Pfam domains (1)
           Pfam domains (2) -------LSM-1mgqG02 G:16-81                                                Pfam domains (2)
           Pfam domains (3) -------LSM-1mgqG03 G:16-81                                                Pfam domains (3)
           Pfam domains (4) -------LSM-1mgqG04 G:16-81                                                Pfam domains (4)
           Pfam domains (5) -------LSM-1mgqG05 G:16-81                                                Pfam domains (5)
           Pfam domains (6) -------LSM-1mgqG06 G:16-81                                                Pfam domains (6)
           Pfam domains (7) -------LSM-1mgqG07 G:16-81                                                Pfam domains (7)
         Sec.struct. author ......hhhhhh....eeeeee....eeeeeeeee.....eeeeeeeeee..eeeeeeeeeee....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                  1mgq G  9 VNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISP 81
                                    18        28        38        48        58        68        78   

   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, 7)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 7)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 7)

Asymmetric/Biological Unit
(-)
Clan: Sm-like (17)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G   (RUXX_METTH | O26745)
biological process
    GO:0000398    mRNA splicing, via spliceosome    The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
cellular component
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0005732    small nucleolar ribonucleoprotein complex    A ribonucleoprotein complex that contains an RNA molecule of the small nucleolar RNA (snoRNA) family and associated proteins. Most are involved in a step of processing of rRNA: cleavage, 2'-O-methylation, or pseudouridylation. The majority, though not all, fall into one of two classes, box C/D type or box H/ACA type.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RUXX_METTH | O267451i81 1jbm 1jri 1loj

(-) Related Entries Specified in the PDB File

1b34 1B34 CONTAINS CRYSTAL STRUCTURE OF A HETERO-DIMERIC HUMAN SM COMPLEX
1d3b 1D3B CONTAINS CRYSTAL STRUCTURE OF A HETERO-DIMERIC HUMAN SM COMPLEX
1i4k 1I4K CONTAINS CRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF- SM1) FROM ARCHAEOGLOBUS FULGIDUS AT 2.5A RESOLUTION
1i5l 1I5L CONTAINS CRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF- SM1) FROM ARCHAEOGLOBUS FULGIDUS COMPLEXED WITH SHORT POLY- U RNA
1i81 1I81 CONTAINS CRYSTAL STRUCTURE OF A HEPTAMERIC LSM PROTEIN FROM METHANOBACTERIUM THERMOAUTOTROPHICUM
1i8f 1I8F CONTAINS THE CRYSTAL STRUCTURE OF A HEPTAMERIC ARCHAEAL SM PROTEIN: IMPLICATIONS FOR THE EUKARYOTIC SNRNP CORE
1jri 1JRI CONTAINS THE CRYSTAL STRUCTURE OF AN SM-LIKE ARCHAEAL PROTEIN WITH TWO HEPTAMERS IN THE ASYMMETRIC UNIT
1kq1 1KQ1 CONTAINS CRYSTAL STRUCTURE OF THE PLEIOTROPIC TRANSLATIONAL REGULATOR, HFQ AT 1.55 A
1ljo 1LJO CONTAINS CRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF- SM2) FROM ARCHAEOGLOBUS FULGIDUS AT 1.95A RESOLUTION