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(-) Description

Title :  CRYSTAL STRUCTURE OF DOMAIN III OF THE CRICKET PARALYSIS VIRUS IRES RNA
 
Authors :  J. S. Kieft, D. A. Costantino, J. S. Pfingsten, R. P. Rambo
Date :  19 Oct 07  (Deposition) - 25 Dec 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ires, Rna Structure, Translation Initiation, Trna Anticodon, Hybrid State, Trna Mimicry (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. A. Costantino, J. S. Pfingsten, R. P. Rambo, J. S. Kieft
Trna-Mrna Mimicry Drives Translation Initiation From A Viral Ires.
Nat. Struct. Mol. Biol. V. 15 57 2008
PubMed-ID: 18157151  |  Reference-DOI: 10.1038/NSMB1351
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RNA (29-MER)
    Chains: A
    Engineered: YES
    Fragment: RESIDUES 6174-6202
    Mutation: YES
    Other Details: CRPV IGR IRES RNA
    Other Details - Source: RNA MADE BY IN VITRO TRANSCRIPTION. THIS NATURALLY OCCURS IN CRICKET PARALYSIS VIRUS
    Synthetic: YES
 
Molecule 2 - RNA (5'- R(P*UP*AP*AP*GP*AP*AP*AP*UP*UP*UP*AP*CP*CP*U)-3')
    Chains: B
    Engineered: YES
    Fragment: RESIDUES 6203-6216
    Other Details: CRPV IGR IRES RNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1IRI3Ligand/IonIRIDIUM HEXAMMINE ION
2PO41Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREU B:6216 , HOH B:6236 , HOH B:6252BINDING SITE FOR RESIDUE PO4 B 6217
2AC2SOFTWAREG A:6175 , U A:6176 , U A:6177 , A A:6197 , U A:6198 , G A:6199 , A A:6200 , HOH A:6275 , HOH A:6276BINDING SITE FOR RESIDUE IRI A 1
3AC3SOFTWAREA A:6182 , G A:6183 , A A:6184 , U A:6185 , U A:6186 , G A:6189 , HOH A:6211 , HOH A:6255 , HOH A:6256 , HOH A:6257BINDING SITE FOR RESIDUE IRI A 2
4AC4SOFTWAREC A:6181 , G A:6183 , A A:6184 , A A:6191 , G A:6192 , U A:6193 , C A:6194 , HOH A:6211 , HOH A:6253 , HOH A:6285BINDING SITE FOR RESIDUE IRI A 3

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3B31)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3B31)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) 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
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Chain A from PDB  Type:RNA  Length:29
                                                              
                3b31 A 6174 GGUUAUUCAGAUUAGGUAGUCGAAUGACC 6202
                                  6183      6193         


Chain B from PDB  Type:RNA  Length:14
                                               
                3b31 B 6203 UAAGAAAUUUACCU 6216
                                  6212
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3B31)

(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

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