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(-) Description

Title :  CRYSTAL STRUCTURE OF ERA IN COMPLEX WITH MGGDPNP, NUCLEOTIDES 1506-1542 OF 16S RIBOSOMAL RNA, AND KSGA
 
Authors :  C. Tu, X. Ji
Date :  26 Mar 11  (Deposition) - 22 Jun 11  (Release) - 06 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Gtpase, Kh Domain, Ribosome, Biogenesis, Gtp, 16S Ribosomal Rna, Gtp Hydrolysis, Hydrolase-Transferase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Tu, X. Zhou, S. G. Tarasov, J. E. Tropea, B. P. Austin, D. S. Waugh, D. L. Court, X. Ji
The Era Gtpase Recognizes The Gaucaccucc Sequence And Binds Helix 45 Near The 3' End Of 16S Rrna.
Proc. Natl. Acad. Sci. Usa V. 108 10156 2011
PubMed-ID: 21646538  |  Reference-DOI: 10.1073/PNAS.1017679108
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GTPASE ERA
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPDONR201
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneAQ_1994, ERA, ERA1
    Organism ScientificAQUIFEX AEOLICUS
    Organism Taxid63363
 
Molecule 2 - RIBOSOMAL RNA SMALL SUBUNIT METHYLTRANSFERASE A
    ChainsB
    EC Number2.1.1.182
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPDONR201
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneAQ_1816, KSGA, RSMA
    Organism ScientificAQUIFEX AEOLICUS
    Organism Taxid63363
    Synonym16S RRNA (ADENINE(1518)-N(6)/ADENINE(1519)-N(6))- DIMETHYLTRANSFERASE, 16S RRNA DIMETHYLADENOSINE TRANSFERASE, 16S RRNA DIMETHYLASE, S-ADENOSYLMETHIONINE-6-N', N'-ADENOSYL(RRNA) DIMETHYLTRANSFERASE
 
Molecule 3 - RNA301
    ChainsC
    EngineeredYES
    Other DetailsTHIS SEQUENCE OCCURS NATURALLY IN AQUIFEX AEOLICUS EXCEPT FOR U1506 THAT IS REPLACED WITH C1506.
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
3MG1Ligand/IonMAGNESIUM ION
4MRD2Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:17 , THR A:38 , GNP A:402 , HOH A:603 , HOH A:616BINDING SITE FOR RESIDUE MG A 401
2AC2SOFTWAREASN A:13 , VAL A:14 , GLY A:15 , LYS A:16 , SER A:17 , THR A:18 , SER A:32 , PRO A:33 , GLY A:36 , THR A:37 , THR A:38 , GLY A:61 , ASN A:123 , LYS A:124 , ASP A:126 , LYS A:127 , SER A:155 , ALA A:156 , LEU A:157 , MG A:401 , HOH A:601 , HOH A:603 , HOH A:616 , HOH A:645BINDING SITE FOR RESIDUE GNP A 402
3AC3SOFTWAREPRO A:117 , VAL A:118 , GLU A:147 , THR A:149 , GLU A:150 , TYR A:172 , HOH A:677BINDING SITE FOR RESIDUE MRD A 503
4AC4SOFTWARETYR A:63 , GLU A:64 , GLU A:105 , ASN A:109 , PHE A:110BINDING SITE FOR RESIDUE MRD A 504
5AC5SOFTWARETHR B:160BINDING SITE FOR RESIDUE ACT B 501
6AC6SOFTWARELYS B:130 , GLU B:134 , GLN B:137 , TYR B:157 , HOH B:673BINDING SITE FOR RESIDUE ACT B 502

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1B:90 -B:120

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly B:40 -Thr B:41
2Val B:167 -Pro B:168

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R9X)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_ERAPS51713 Era-type guanine nucleotide-binding (G) domain profile.ERA_AQUAE2-175  1A:2-175
2RRNA_A_DIMETHPS01131 Ribosomal RNA adenine dimethylases signature.RSMA_AQUAE34-62  1B:34-62
3KH_TYPE_2PS50823 Type-2 KH domain profile.ERA_AQUAE206-285  1A:206-285

(-) Exons   (0, 0)

(no "Exon" information available for 3R9X)

(-) 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:302
 aligned with ERA_AQUAE | O67800 from UniProtKB/Swiss-Prot  Length:301

    Alignment length:302
                             1                                                                                                                                                                                                                                                                                                            
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299  
           ERA_AQUAE      - -MKVGYVAIVGKPNVGKSTLLNNLLGTKVSIISPKAGTTRMRVLGVKNIPNEAQIIFLDTPGIYEPKKSDVLGHSMVEIAKQSLEEADVILFMIDATEGWRPRDEEIYQNFIKPLNKPVIVVINKIDKIGPAKNVLPLIDEIHKKHPELTEIVPISALKGANLDELVKTILKYLPEGEPLFPEDMITDLPLRLLAAEIVREKAMMLTREEVPTSIAVKINEIKPGDANPNMLVIKGEIIVDRENLKPIIIGKKGQRLKEIGKRARQELELILGRPVYLELWVKVVPDWRRRPEYVRLFGYAL  301
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----MMR_HSR1-3r9xA02 A:5-124                                                                                                ------------------------------------------------------------------------------------KH_2-3r9xA01 A:209-288                                                          ------------- Pfam domains
         Sec.struct. author ..eeeeeeee.....hhhhhhhhhhh................eeeeeee...eeeeeee..........hhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhhhhhhhhhh..eeeeeehhhhh.hhhhhhhhhhhhhhhh.....eee.......hhhhhhhhhhh.................hhhhhhhhhhhhhhhhh....hhhhheeeeeeeeee..eeeeeeeeeeeee.hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..eeeeeeeee..hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --G_ERA  PDB: A:2-175 UniProt: 2-175                                                                                                                                            ------------------------------KH_TYPE_2  PDB: A:206-285 UniProt: 206-285                                      ---------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3r9x A    0 HMKVGYVAIVGKPNVGKSTLLNNLLGTKVSIISPKAGTTRMRVLGVKNIPNEAQIIFLDTPGIYEPKKSDVLGHSMVEIAKQSLEEADVILFMIDATEGWRPRDEEIYQNFIKPLNKPVIVVINKIDKIGPAKNVLPLIDEIHKKHPELTEIVPISALKGANLDELVKTILKYLPEGEPLFPEDMITDLPLRLLAAEIVREKAMMLTREEVPTSIAVKINEIKPGDANPNMLVIKGEIIVDRENLKPIIIGKKGQRLKEIGKRARQELELILGRPVYLELWVKVVPDWRRRPEYVRLFGYAL  301
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299  

Chain B from PDB  Type:PROTEIN  Length:235
 aligned with RSMA_AQUAE | O67680 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:235
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242     
          RSMA_AQUAE     13 LVSEGVLKKIAEELNIEEGNTVVEVGGGTGNLTKVLLQHPLKKLYVIELDREMVENLKSIGDERLEVINEDASKFPFCSLGKELKVVGNLPYNVASLIIENTVYNKDCVPLAVFMVQKEVAEKLQGKKDTGWLSVFVRTFYDVNYVMTVPPRFFVPPPKVQSAVIKLVKNEKFPVKDLKNYKKFLTKIFQNRRKVLRKKIPEELLKEAGINPDARVEQLSLEDFFKLYRLIEDSG  247
               SCOP domains d3r9xb_ B: automated matches                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains RrnaAD-3r9xB01 B:13-245                                                                                                                                                                                                                  -- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.......eeee....hhhhhhhhhh....eeee....hhhhhhhhh....eee........hhhhh....eeeee.hhhhhhhhhhhhhhh.....eeeeeeehhhhhhhhh....hhhhhhhhhheeeeeeeeehhhhh.......eeeeeeee.......hhhhhhhhhhhhhh....hhhhh.hhhhhhhh......hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------RRNA_A_DIMETH  PDB: B:34-62  ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3r9x B   13 LVSEGVLKKIAEELNIEEGNTVVEVGGGTGNLTKVLLQHPLKKLYVIELDREMVENLKSIGDERLEVINEDASKFPFCSLGKELKVVGNLPYNVASLIIENTVYNKDCVPLAVFMVQKEVAEKLQGKKDTGWLSVFVRTFYDVNYVMTVPPRFFVPPPKVQSAVIKLVKNEKFPVKDLKNYKKFLTKIFQNRRKVLRKKIPEELLKEAGINPDARVEQLSLEDFFKLYRLIEDSG  247
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242     

Chain C from PDB  Type:RNA  Length:35
                                                                    
                3r9x C 1506 CAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCU 1540
                                  1515      1525      1535     

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R9X)

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Clan: KH (43)
(-)
Family: KH_2 (20)

(-) Gene Ontology  (22, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ERA_AQUAE | O67800)
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:0019843    rRNA binding    Interacting selectively and non-covalently with ribosomal RNA.
    GO:0070181    small ribosomal subunit rRNA binding    Interacting selectively and non-covalently with the small ribosomal subunit RNA (SSU rRNA), a constituent of the small ribosomal subunit. In S. cerevisiae, this is the 18S rRNA.
biological process
    GO:0042274    ribosomal small subunit biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a small ribosomal subunit; includes transport to the sites of protein synthesis.
    GO:0042254    ribosome biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain B   (RSMA_AQUAE | O67680)
molecular function
    GO:0052908    16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity    Catalysis of the reaction: 4 S-adenosyl-L-methionine + adenine(1518)/adenine(1519) in 16S rRNA = 4 S-adenosyl-L-homocysteine + N(6)-dimethyladenine(1518)/N(6)-dimethyladenine(1519) in 16S rRNA.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0016433    rRNA (adenine) methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing methyladenine.
    GO:0000179    rRNA (adenine-N6,N6-)-dimethyltransferase activity    Catalysis of the dimethylation two adjacent A residues in the loop closing the 3'-terminal stem of the 18S rRNA, using S-adenosyl-L-methionine as a methyl donor.
    GO:0008649    rRNA methyltransferase activity    Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a nucleoside residue in an rRNA molecule.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0031167    rRNA methylation    The posttranscriptional addition of methyl groups to specific residues in an rRNA molecule.
    GO:0000154    rRNA modification    The covalent alteration of one or more nucleotides within an rRNA molecule to produce an rRNA molecule with a sequence that differs from that coded genetically.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
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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 Related Entries

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

UniProtKB/Swiss-Prot
        ERA_AQUAE | O678003iev 3r9w
        RSMA_AQUAE | O676803ftc 3ftd 3fte 3ftf

(-) Related Entries Specified in the PDB File

1ega CRYSTAL STRUCTURE OF ERA
3ieu CRYSTAL STRUCTURE OF ERA IN COMPLEX WITH GDP
3iev CRYSTAL STRUCTURE OF ERA IN COMPLEX WITH MGGDPNP AND NUCLEOTIDES 1531-1542 OF 16S RIBOSOMAL RNA
3r9w