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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FMN RIBOSWITCH BOUND TO ROSEOFLAVIN
 
Authors :  A. A. Serganov, L. Huang
Date :  31 Oct 08  (Deposition) - 27 Jan 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  X,Y
Keywords :  Roseoflavin, Fmn, Riboswitch, Transcription, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Serganov, L. Huang, D. J. Patel
Coenzyme Recognition And Gene Regulation By A Flavin Mononucleotide Riboswitch.
Nature V. 458 233 2009
PubMed-ID: 19169240  |  Reference-DOI: 10.1038/NATURE07642

(-) Compounds

Molecule 1 - FMN RIBOSWITCH
    Chains: X
    Engineered: YES
    Mutation: YES
    Other Details: FMN RIBOSWITCH, 5' STRAND
    Other Details - Source: IN VITRO TRANSCRIBED RNA FROM THE FUSOBACTERIUM NUCLEATUM IMPX GENE
    Synthetic: YES
 
Molecule 2 - FMN RIBOSWITCH
    Chains: Y
    Engineered: YES
    Other Details: FMN RIBOSWITCH, 3' STRAND
    Other Details - Source: IN VITRO TRANSCRIBED RNA FROM THE FUSOBACTERIUM NUCLEATUM IMPX GENE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : XY

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric/Biological Unit (3, 14)
No.NameCountTypeFull Name
1K2Ligand/IonPOTASSIUM ION
2MG11Ligand/IonMAGNESIUM ION
3RS31Ligand/Ion1-DEOXY-1-[8-(DIMETHYLAMINO)-7-METHYL-2,4-DIOXO-3,4-DIHYDROBENZO[G]PTERIDIN-10(2H)-YL]-D-RIBITOL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREG X:10 , G X:11 , G X:12 , A X:48 , A X:49 , U Y:61 , G Y:84 , A Y:85 , A Y:99BINDING SITE FOR RESIDUE RS3 Y 200
2AC2SOFTWAREG X:36 , U X:37 , A X:40BINDING SITE FOR RESIDUE K X 300
3AC3SOFTWAREG Y:98BINDING SITE FOR RESIDUE K Y 301
4AC4SOFTWAREU Y:89 , A Y:92BINDING SITE FOR RESIDUE MG Y 305
5AC5SOFTWAREC X:13 , A X:14BINDING SITE FOR RESIDUE MG X 306
6AC6SOFTWAREG X:28BINDING SITE FOR RESIDUE MG X 310
7AC7SOFTWAREA X:22 , U X:23BINDING SITE FOR RESIDUE MG X 314
8AC8SOFTWAREC X:13 , A X:14BINDING SITE FOR RESIDUE MG X 315

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3F4H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3F4H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3F4H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3F4H)

(-) Exons   (0, 0)

(no "Exon" information available for 3F4H)

(-) 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 X from PDB  Type:DNA/RNA  Length:54
                                                                                      
                 3f4h X   1 GGAUCUUCGGGGCAGGGUGAAAUUCCCGACCGGUGGUAUAGUCCACGAAAGCUU  54
                                    10        20        30        40        50    


Chain Y from PDB  Type:RNA  Length:56
                                                                                        
                 3f4h Y  57 GCUUUGAUUUGGUGAAAUUCCAAAACCGACAGUAGAGUCUGGAUGAGAGAAGAUUC 112
                                    66        76        86        96       106
   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  (0, 0)

(no "SCOP Domain" information available for 3F4H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3F4H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3F4H)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3F4H)

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  3f4h
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 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3F4H)

(-) Related Entries Specified in the PDB File

3f2q FMN BOUND, NATIVE DATA SET
3f2t FMN BOUND, IRIDIUM SOAK
3f2w FMN BOUND, BARIUM SOAK
3f2x FMN BOUND, CESIUM SOAK
3f2y FMN BOUND, MANGANESE SOAK
3f30 FMN BOUND, COBALT SOAK
3f4e FMN BOUND, NATIVE DATA SET, SPLIT RNA
3f4g RIBOFLAVIN BOUND, NATIVE DATA SET, SPLIT RNA