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(-) Description

Title :  HEPTAMERIC CRYSTAL STRUCTURE OF MTH649, AN SM-LIKE ARCHAEAL PROTEIN FROM METHANOBACTERIUM THERMAUTOTROPHICUM
 
Authors :  C. Mura, D. Eisenberg
Date :  06 Jun 01  (Deposition) - 25 Mar 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G
Keywords :  Ring-Shaped Homoheptamer, All Beta-Strand, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Mura, A. Kozhukhovsky, M. Gingery, M. Phillips, D. Eisenberg
The Oligomerization And Ligand-Binding Properties Of Sm-Like Archaeal Proteins (Smaps)
Protein Sci. V. 12 832 2003
PubMed-ID: 12649441  |  Reference-DOI: 10.1110/PS.0224703
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE SNRNP SM-LIKE PROTEIN
    ChainsA, B, C, D, E, F, G
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET-22B(+)
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentFULL-LENGTH SM PROTEIN
    GeneMTH0649 ORF
    Organism ScientificMETHANOTHERMOBACTER THERMAUTOTROPHICUS
    Organism Taxid145262

 Structural Features

(-) Chains, Units

  1234567
Asymmetric/Biological Unit ABCDEFG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 16)

Asymmetric/Biological Unit (2, 16)
No.NameCountTypeFull Name
1ACY5Ligand/IonACETIC ACID
2EDO11Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL C:11 , GLN C:12 , PHE D:43 , ASP D:44 , LEU D:45BINDING SITE FOR RESIDUE EDO D 2001
02AC2SOFTWAREVAL F:39 , ASN F:52 , ASP F:53 , HOH F:2028BINDING SITE FOR RESIDUE EDO F 2002
03AC3SOFTWARELYS E:29 , VAL E:77 , ACY E:1003 , HOH E:2057 , ARG F:34 , GLU F:56 , HOH F:2023BINDING SITE FOR RESIDUE EDO F 2003
04AC4SOFTWAREVAL C:39 , LYS C:41 , ASN C:52 , ASP C:53BINDING SITE FOR RESIDUE EDO C 2004
05AC5SOFTWAREGLY A:19 , ASN E:23BINDING SITE FOR RESIDUE EDO E 2005
06AC6SOFTWARELEU D:30 , LYS D:31 , ARG D:34 , ASN D:75BINDING SITE FOR RESIDUE EDO D 2006
07AC7SOFTWARELEU B:45 , HIS B:46 , HOH B:110 , HIS C:46 , ASN C:48 , ARG C:72BINDING SITE FOR RESIDUE EDO C 2007
08AC8SOFTWAREVAL D:77 , ACY D:1004 , HOH D:2011 , LEU E:30 , LYS E:31 , ASN E:75 , HOH E:2041BINDING SITE FOR RESIDUE EDO E 2008
09AC9SOFTWARETHR G:68BINDING SITE FOR RESIDUE EDO F 2009
10BC1SOFTWARELEU F:45 , HIS G:46 , EDO G:2011BINDING SITE FOR RESIDUE EDO G 2010
11BC2SOFTWARELEU F:45 , HIS F:46 , ASN G:48 , ARG G:72 , EDO G:2010 , HOH G:2017 , HOH G:2049BINDING SITE FOR RESIDUE EDO G 2011
12BC3SOFTWAREALA C:17 , SER C:21 , SER C:80 , ARG C:81 , THR D:68BINDING SITE FOR RESIDUE ACY C 1001
13BC4SOFTWAREALA A:17 , SER A:21 , SER A:80 , HOH A:1036 , THR B:68 , LEU B:70BINDING SITE FOR RESIDUE ACY A 1002
14BC5SOFTWARELYS E:31 , GLY E:32 , ARG F:34 , EDO F:2003BINDING SITE FOR RESIDUE ACY E 1003
15BC6SOFTWAREGLY D:32 , HOH D:2011 , HOH D:2021 , EDO E:2008BINDING SITE FOR RESIDUE ACY D 1004
16BC7SOFTWAREGLN F:12 , ARG F:13 , SER G:42 , PHE G:43BINDING SITE FOR RESIDUE ACY F 1005

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1JBM)

(-) 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:78
 aligned with RUXX_METTH | O26745 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:78
                                                                                                   81     
                                    18        28        38        48        58        68        78  |     
            RUXX_METTH    9 VNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISP-----  -
               SCOP domains d1jbma_ A: Archaeal homoheptameric Sm protein                                  SCOP domains
               CATH domains 1jbmA00 A:9-86  [code=2.30.30.100, no name defined]                            CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhh....eeeeee...eeeeeeeeee.....eeeeeeeeee..eeeeeeeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                  1jbm A  9 VNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISRGKLAA 86
                                    18        28        38        48        58        68        78        

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

    Alignment length:73
                                                                                                  81 
                                    19        29        39        49        59        69        79 | 
            RUXX_METTH   10 NVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISP-  -
               SCOP domains d1jbmb_ B: Archaeal homoheptameric Sm protein                             SCOP domains
               CATH domains 1jbmB00 B:10-82  [code=2.30.30.100, no name defined]                      CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh....eeeeee....eeeeeeeee.....eeeeeeeee....eeeeeeeeee....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                  1jbm B 10 NVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISRG 82
                                    19        29        39        49        59        69        79   

Chain C from PDB  Type:PROTEIN  Length:77
 aligned with RUXX_METTH | O26745 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:77
                                                                                                  81     
                                    19        29        39        49        59        69        79 |     
            RUXX_METTH   10 NVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISP-----  -
               SCOP domains d1jbmc_ C: Archaeal homoheptameric Sm protein                                 SCOP domains
               CATH domains 1jbmC00 C:10-86  [code=2.30.30.100, no name defined]                          CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh..eeeeee....eeeeeeeee.....eeeeeeeeee..eeeeeeeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                  1jbm C 10 NVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISRGKLAA 86
                                    19        29        39        49        59        69        79       

Chain D from PDB  Type:PROTEIN  Length:71
 aligned with RUXX_METTH | O26745 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:71
                                    20        30        40        50        60        70        80 
            RUXX_METTH   11 VQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISP 81
               SCOP domains d1jbmd_ D: Archaeal homoheptameric Sm protein                           SCOP domains
               CATH domains 1jbmD00 D:11-81  [code=2.30.30.100, no name defined]                    CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh..eeeeee....eeeeeeeee.....eeeeeeeeee..eeeeeeeeeee....eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  1jbm D 11 VQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISR 81
                                    20        30        40        50        60        70        80 

Chain E from PDB  Type:PROTEIN  Length:75
 aligned with RUXX_METTH | O26745 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:75
                                                                                                   81  
                                    18        28        38        48        58        68        78  |  
            RUXX_METTH    9 VNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISP--  -
               SCOP domains d1jbme_ E: Archaeal homoheptameric Sm protein                               SCOP domains
               CATH domains 1jbmE00 E:9-83  [code=2.30.30.100, no name defined]                         CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhh....eeeeee....eeeeeeeee.....eeeeeeeeee..eeeeeeeeeee....eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                  1jbm E  9 VNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISRGK 83
                                    18        28        38        48        58        68        78     

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

    Alignment length:73
                                                                                                 81  
                                    20        30        40        50        60        70        80|  
            RUXX_METTH   11 VQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISP--  -
               SCOP domains d1jbmf_ F: Archaeal homoheptameric Sm protein                             SCOP domains
               CATH domains 1jbmF00 F:11-83  [code=2.30.30.100, no name defined]                      CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh..eeeeee...eeeeeeeeee.....eeeeeeeeee..eeeeeeeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                  1jbm F 11 VQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISRGK 83
                                    20        30        40        50        60        70        80   

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

    Alignment length:74
                                                                                                81    
                                    21        31        41        51        61        71        81    
            RUXX_METTH   12 QRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISP----  -
               SCOP domains d1jbmg_ G: Archaeal homoheptameric Sm protein                              SCOP domains
               CATH domains 1jbmG00 G:12-85  [code=2.30.30.100, no name defined]                       CATH domains
           Pfam domains (1) ----LSM-1jbmG01 G:16-80                                              ----- Pfam domains (1)
           Pfam domains (2) ----LSM-1jbmG02 G:16-80                                              ----- Pfam domains (2)
           Pfam domains (3) ----LSM-1jbmG03 G:16-80                                              ----- Pfam domains (3)
           Pfam domains (4) ----LSM-1jbmG04 G:16-80                                              ----- Pfam domains (4)
           Pfam domains (5) ----LSM-1jbmG05 G:16-80                                              ----- Pfam domains (5)
           Pfam domains (6) ----LSM-1jbmG06 G:16-80                                              ----- Pfam domains (6)
           Pfam domains (7) ----LSM-1jbmG07 G:16-80                                              ----- Pfam domains (7)
         Sec.struct. author .hhhhhhhh....eeeeee....eeeeeeeee.....eeeeeeeeee..eeeeeeeeeee....eeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                  1jbm G 12 QRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISRGKLA 85
                                    21        31        41        51        61        71        81    

   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 1jri 1loj 1mgq

(-) Related Entries Specified in the PDB File

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1d3b CRYSTAL STRUCTURE OF THE D3B HUMAN SM PROTEIN HETERODIMER
1i81 CRYSTAL STRUCTURE OF THE SAME SM-LIKE ARCHAEAL PROTEIN (IN SPACEGROUP P21, NOT P1), DETERMINED INDEPENDENTLY BY ANOTHER GROUP
1i8f CRYSTAL STRUCTURE OF A CLOSELY RELATED, HEPTAMERIC SM-LIKE ARCHAEAL PROTEIN FROM PYROBACULUM AEROPHILUM