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(-) Description

Title :  CRYSTAL STRUCTURE OF TWISTER WITH THE NUCLEOTIDE 5'- TO THE CLEAVAGE SITE DISORDERED AT 3.1 A RESOLUTION
 
Authors :  D. R. Eiler, J. Wang, T. A. Steitz
Date :  03 Jun 14  (Deposition) - 03 Sep 14  (Release) - 24 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Keywords :  Self-Cleaving Ribozyme, 2' Deoxy Subsitution, Nucleotide 5 (U), Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Eiler, J. Wang, T. A. Steitz
Structural Basis For The Fast Self-Cleavage Reaction Catalyzed By The Twister Ribozyme.
Proc. Natl. Acad. Sci. Usa V. 111 13028 2014
PubMed-ID: 25157168  |  Reference-DOI: 10.1073/PNAS.1414571111

(-) Compounds

Molecule 1 - TWISTER RNA SEQUENCE
    Chains: A, C, E, G
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - TWISTER RNA SEQUENCE
    Chains: B, D, F, H
    Engineered: YES
    Other Details: RNA WAS PREPARED BY IN VITRO TRANSCRIPTION WITH T7 RNA POLYMERASE.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB      
Biological Unit 2 (1x):   CD    
Biological Unit 3 (1x):     EF  
Biological Unit 4 (1x):       GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1GTP4Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
2MG4Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GTP1Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GTP1Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1GTP1Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1GTP1Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREG A:18BINDING SITE FOR RESIDUE MG A 101
2AC2SOFTWAREGTP F:27BINDING SITE FOR RESIDUE MG F 101
3AC3SOFTWAREU F:72 , U G:3BINDING SITE FOR RESIDUE MG F 102
4AC4SOFTWAREG H:54BINDING SITE FOR RESIDUE MG H 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric 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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Chain A from PDB  Type:DNA/RNA  Length:24
                                                       
                  4qjd A  3 UGUAACUCCGCCUAUGUCAUCUUA 26
                                    12        22    


Chain B from PDB  Type:RNA  Length:47
                                                                              
                  4qjd B 27 gUAAAUGAUAUAGCCGGUCCCAAGCCCGGAAAAAGGAGGAGGGUAUA 73
                            |       36        46        56        66       
                           27-GTP                                          


Chain C from PDB  Type:DNA/RNA  Length:25
                                                        
                  4qjd C  1 UAUGUAACUCCGCCUAUGUCAUCUU 25
                                    10        20     


Chain D from PDB  Type:RNA  Length:47
                                                                              
                  4qjd D 27 gUAAAUGAUAUAGCCGGUCCCAAGCCCGGAAAAAGGAGGAGGGUAUA 73
                            |       36        46        56        66       
                           27-GTP                                          


Chain E from PDB  Type:DNA/RNA  Length:26
                                                         
                  4qjd E  1 UAUGUAACUCCGCCUAUGUCAUCUUA 26
                                    10        20      


Chain F from PDB  Type:RNA  Length:47
                                                                              
                  4qjd F 27 gUAAAUGAUAUAGCCGGUCCCAAGCCCGGAAAAAGGAGGAGGGUAUA 73
                            |       36        46        56        66       
                           27-GTP                                          


Chain G from PDB  Type:DNA/RNA  Length:25
                                                        
                  4qjd G  1 UAUGUAACUCCGCCUAUGUCAUCUU 25
                                    10        20     


Chain H from PDB  Type:RNA  Length:47
                                                                              
                  4qjd H 27 gUAAAUGAUAUAGCCGGUCCCAAGCCCGGAAAAAGGAGGAGGGUAUA 73
                            |       36        46        56        66       
                           27-GTP
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

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4qjh