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(-) Description

Title :  CRYSTAL STRUCTURE OF RNA R(GCUGCUGC) WITH ANTISENSE PNA P(GCAGCAGC)
 
Authors :  A. Kiliszek, K. Banaszak, Z. Dauter, W. Rypniewski
Date :  06 Nov 15  (Deposition) - 13 Jan 16  (Release) - 17 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.14
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cug Repeats, Rna/Pna Duplex, Antisense Pna, Myotonic Dystrophy Type 1, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kiliszek, K. Banaszak, Z. Dauter, W. Rypniewski
The First Crystal Structures Of Rna-Pna Duplexes And A Pna-Pna Duplex Containing Mismatches-Toward Anti-Sense Therapy Against Treds.
Nucleic Acids Res. V. 44 1937 2016
PubMed-ID: 26717983  |  Reference-DOI: 10.1093/NAR/GKV1513

(-) Compounds

Molecule 1 - RNA (5'-R(*GP*CP*UP*GP*CP*UP*GP*C)-3')
    Chains: A
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS.
    Synthetic: YES
 
Molecule 2 - ANTISENSE PNA P(GCAGCAGC)
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1APN2OTHER2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-ADENINE
2CL2Ligand/IonCHLORIDE ION
3CPN3OTHER2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-CYTOSINE
4GPN3OTHER2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-GUANINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREC A:2 , HOH A:206 , HOH A:260 , GPN B:101 , HOH B:313 , HOH B:316binding site for residue CL A 101
2AC2SOFTWAREGPN B:107binding site for residue CL B 201
3AC3SOFTWAREG A:1 , C A:2 , G A:7 , C A:8 , CL A:101 , HOH A:234 , APN B:103 , GPN B:107 , CPN B:108 , HOH B:308 , HOH B:317 , HOH B:321 , HOH B:325 , HOH B:326 , HOH B:327 , HOH B:328 , HOH B:332binding site for residues GPN B 101 and CPN B 102
4AC4SOFTWAREG A:1 , U A:6 , G A:7 , C A:8 , HOH A:234 , GPN B:101 , GPN B:104 , CPN B:108 , HOH B:308 , HOH B:310 , HOH B:319 , HOH B:320 , HOH B:324 , HOH B:328 , HOH B:332binding site for residues CPN B 102 and APN B 103
5AC5SOFTWAREG A:1 , G A:4 , C A:5 , U A:6 , G A:7 , CPN B:102 , CPN B:105 , CPN B:108 , HOH B:302 , HOH B:303 , HOH B:306 , HOH B:307 , HOH B:310 , HOH B:319 , HOH B:320 , HOH B:324binding site for residues APN B 103 and GPN B 104
6AC6SOFTWAREG A:4 , C A:5 , U A:6 , APN B:103 , APN B:106 , HOH B:301 , HOH B:302 , HOH B:303 , HOH B:304 , HOH B:306 , HOH B:307 , HOH B:320 , HOH B:329 , HOH B:330binding site for residues GPN B 104 and CPN B 105
7AC7SOFTWAREU A:3 , G A:4 , C A:5 , GPN B:104 , GPN B:107 , HOH B:301 , HOH B:304 , HOH B:312 , HOH B:315 , HOH B:318 , HOH B:329 , HOH B:330binding site for residues CPN B 105 and APN B 106
8AC8SOFTWAREC A:2 , U A:3 , G A:4 , G A:7 , C A:8 , GPN B:101 , CPN B:105 , CPN B:108 , CL B:201 , HOH B:305 , HOH B:309 , HOH B:311 , HOH B:312 , HOH B:314 , HOH B:315 , HOH B:318 , HOH B:323 , HOH B:329binding site for residues APN B 106 and GPN B 107
9AC9SOFTWAREG A:1 , C A:2 , U A:3 , G A:7 , C A:8 , GPN B:101 , CPN B:102 , APN B:103 , APN B:106 , CL B:201 , HOH B:305 , HOH B:309 , HOH B:311 , HOH B:313 , HOH B:314 , HOH B:315 , HOH B:316 , HOH B:322 , HOH B:323 , HOH B:331 , HOH B:339binding site for residues GPN B 107 and CPN B 108

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5EMF)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5EMF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EMF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EMF)

(-) Exons   (0, 0)

(no "Exon" information available for 5EMF)

(-) 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:RNA  Length:8
                                        
                 5emf A   1 GCUGCUGC   8


Chain B from PDB  Type:OTHER  Length:8
                                        
                 5emf B 101 xxxxxxxx 108
                            ||||||||
                          101-GPN|||
                           102-CPN||
                            103-APN|
                             104-GPN
                              105-CPN
                               106-APN
                                107-GPN
                                 108-CPN
   Legend:   → Mismatch (orange background)
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  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 5EMF)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EMF)

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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(-) Related Entries Specified in the PDB File

5eme A SIMILAR DUPLEX OF RNA AND PNA.