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(-) Description

Title :  CRYSTAL STRUCTURE OF BACILLUS SUBTILIS CYCLIC-DI-AMP RIBOSWITCH YDAO
 
Authors :  C. P. Jones, A. R. Ferre-D'Amare
Date :  26 Aug 14  (Deposition) - 22 Oct 14  (Release) - 25 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.21
Chains :  Asym./Biol. Unit :  B,C
Keywords :  Riboswitch, Cyclic-Di-Amp, Protein-Rna Complex, Rna Binding Protein- Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. P. Jones, A. R. Ferre-D'Amare
Crystal Structure Of A C-Di-Amp Riboswitch Reveals An Internally Pseudo-Dimeric Rna.
Embo J. V. 33 2692 2014
PubMed-ID: 25271255  |  Reference-DOI: 10.15252/EMBJ.201489209

(-) Compounds

Molecule 1 - U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PIDTBLUE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 6-96
    Gene: SNRPA
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: U1A
 
Molecule 2 - C-DI-AMP RIBSOSWITCH
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : BC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 12)

Asymmetric/Biological Unit (5, 12)
No.NameCountTypeFull Name
12BA2Ligand/Ion(2R,3R,3AS,5R,7AR,9R,10R,10AS,12R,14AR)-2,9-BIS(6-AMINO-9H-PURIN-9-YL)OCTAHYDRO-2H,7H-DIFURO[3,2-D:3',2'-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-3,5,10,12-TETROL 5,12-DIOXIDE
2EDO1Ligand/Ion1,2-ETHANEDIOL
3K1Ligand/IonPOTASSIUM ION
4MG5Ligand/IonMAGNESIUM ION
5MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 4W92)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4W92)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4W92)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4W92)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4W92)

(-) Exons   (0, 0)

(no "Exon" information available for 4W92)

(-) 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 B from PDB  Type:PROTEIN  Length:90
                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeee......hhhhhhhhhhhhhhhhh.eeeeee........eeeeee.hhhhhhhhhhhhh..ee..ee.eeee...hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 4w92 B   6 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKmRGQAFVIFKEVSSATNALRSmQGFPFYDKPmRIQYATDSDIIAK  96
                                    15        25        35        45     |  55        65      | 75      | 85 ||     96
                                                                        51-MSE               72-MSE    82-MSE7|       
                                                                                                             89       


Chain C from PDB  Type:DNA/RNA  Length:96
                                                                                                                                
                 4w92 C   1 GCGCGCUUAAUCUGCAGAGCGGGGGACCCAUUGCACUCAGGGGUGAAUCCUGGUAGGGCGAAAGCCCGAAUCCGUCAGCUAACCUCGUAAGCGCGC 119
                                    10   ||   24        34       |58        68||      83        93       103       113      
                                        14|                     42|          69|                                            
                                         19                      57           75
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4W92)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4W92)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4W92)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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  4w92
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  SNRPA_HUMAN | P09012
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 Related Entries

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

UniProtKB/Swiss-Prot
        SNRPA_HUMAN | P09012: 1aud 1drz 1dz5 1fht 1m5k 1m5o 1m5p 1m5v 1nu4 1oia 1sj3 1sj4 1sjf 1u6b 1urn 1vbx 1vby 1vbz 1vc0 1vc5 1vc6 1zzn 2a3j 2nz4 2oih 2oj3 2u1a 3bo2 3bo3 3bo4 3cul 3cun 3egz 3g8s 3g8t 3g96 3g9c 3hhn 3iin 3irw 3iwn 3k0j 3l3c 3mum 3mur 3mut 3muv 3mxh 3p49 3pgw 3r1h 3r1l 3ucu 3ucz 3ud3 3ud4 3utr 4c4w 4pr6 4prf 4w90 4yb1 5ddo 5ddp 5ddq 5ddr 5fj4

(-) Related Entries Specified in the PDB File

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