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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FMN RIBOSWITCH BOUND TO RIBOFLAVIN.
 
Authors :  A. A. Serganov, L. Huang
Date :  31 Oct 08  (Deposition) - 27 Jan 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.01
Chains :  Asym./Biol. Unit :  X,Y
Keywords :  Riboflavin, 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, 18)

Asymmetric/Biological Unit (3, 18)
No.NameCountTypeFull Name
1K2Ligand/IonPOTASSIUM ION
2MG15Ligand/IonMAGNESIUM ION
3RBF1Ligand/IonRIBOFLAVIN

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREG X:10 , G X:11 , A X:48 , A X:49 , U Y:61 , G Y:84 , A Y:85 , G Y:93 , G Y:98 , A Y:99 , K Y:301BINDING SITE FOR RESIDUE RBF Y 200
02AC2SOFTWAREG X:36 , U X:37BINDING SITE FOR RESIDUE K X 300
03AC3SOFTWAREG Y:97 , G Y:98 , RBF Y:200BINDING SITE FOR RESIDUE K Y 301
04AC4SOFTWAREG X:19BINDING SITE FOR RESIDUE MG X 302
05AC5SOFTWAREG Y:84BINDING SITE FOR RESIDUE MG Y 303
06AC6SOFTWAREU Y:89 , A Y:92BINDING SITE FOR RESIDUE MG Y 305
07AC7SOFTWAREA X:14 , G X:15BINDING SITE FOR RESIDUE MG X 306
08AC8SOFTWAREG Y:68BINDING SITE FOR RESIDUE MG Y 309
09AC9SOFTWAREG X:28BINDING SITE FOR RESIDUE MG X 310
10BC1SOFTWAREA X:22 , U X:23BINDING SITE FOR RESIDUE MG X 314
11BC2SOFTWAREA X:49BINDING SITE FOR RESIDUE MG X 318
12BC3SOFTWAREG X:12 , C Y:95BINDING SITE FOR RESIDUE MG Y 319
13BC4SOFTWAREG Y:91BINDING SITE FOR RESIDUE MG Y 321

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3F4G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3F4G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3F4G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3F4G)

(-) Exons   (0, 0)

(no "Exon" information available for 3F4G)

(-) 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    
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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
                                                                                      
                 3f4g X   1 GGAUCUUCGGGGCAGGGUGAAAUUCCCGACCGGUGGUAUAGUCCACGAAAGCUU  54
                                    10        20        30        40        50    


Chain Y from PDB  Type:RNA  Length:56
                                                                                        
                 3f4g Y  57 GCUUUGAUUUGGUGAAAUUCCAAAACCGACAGUAGAGUCUGGAUGAGAGAAGAUUC 112
                                    66        76        86        96       106
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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 3F4G)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3F4G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3F4G)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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 Related Entries

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

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(-) 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
3f4h ROSEOFLAVIN BOUND