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(-) Description

Title :  THE CRYSTAL STRUCTURE OF AN ALL-RNA MINIMAL HAIRPIN RIBOZYME WITH MUTANT G8I AT THE CLEAVAGE SITE
 
Authors :  J. E. Wedekind
Date :  20 Apr 05  (Deposition) - 14 Feb 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.33
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hairpin Ribozyme, All-Rna, Cobalt Hexaamine, Mutation, Inosine, U39C, Junctionless, Low Salt, S-Turn, E-Loop, Ribose Zipper, Catalytic Rna, 2'-Ome, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Salter, J. Krucinska, S. Alam, V. Grum-Tokars, J. E. Wedekind
Water In The Active Site Of An All-Rna Hairpin Ribozyme And Effects Of Gua8 Base Variants On The Geometry Of Phosphoryl Transfer.
Biochemistry V. 45 686 2006
PubMed-ID: 16411744  |  Reference-DOI: 10.1021/BI051887K
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-R(*UP*CP*CP*CP*(A2M)P*GP*UP*CP*CP*AP*CP*CP*G)-3'
    Chains: A
    Engineered: YES
    Other Details: DERIVED FROM SATELLITE TOBACCO RINGSPOT VIRUS
    Synthetic: YES
 
Molecule 2 - 5'-R(*CP*GP*GP*UP*GP*AP*IP*AP*AP*GP*GP*G)-3'
    Chains: B
    Engineered: YES
    Mutation: YES
    Other Details: DERIVED FROM SATELLITE TOBACCO RINGSPOT VIRUS
    Synthetic: YES
 
Molecule 3 - 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)- 3'
    Chains: C
    Engineered: YES
    Other Details: DERIVED FROM SATELLITE TOBACCO RINGSPOT VIRUS
    Synthetic: YES
 
Molecule 4 - 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP *C)-3'
    Chains: D
    Engineered: YES
    Mutation: YES
    Other Details: DERIVED FROM SATELLITE TOBACCO RINGSPOT VIRUS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1A2M1Mod. Nucleotide2'-O-METHYLADENOSINE 5'-(DIHYDROGEN PHOSPHATE)
2NCO2Ligand/IonCOBALT HEXAMMINE(III)
3SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREC A:2 , NCO B:102BINDING SITE FOR RESIDUE SO4 A 103
2AC2SOFTWAREA C:20 , G C:21 , A D:40 , U D:41BINDING SITE FOR RESIDUE NCO D 101
3AC3SOFTWARESO4 A:103 , G B:11 , G B:12 , G B:13BINDING SITE FOR RESIDUE NCO B 102

(-) SS Bonds  (0, 0)

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(-) 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/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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Chain A from PDB  Type:RNA  Length:13
                                            
                  1zft A  1 UCCCaGUCCACCG 13
                                |   10   
                                |        
                                5-A2M    


Chain B from PDB  Type:RNA  Length:11
                                          
                  1zft B  2 CGGUGAAAGGG 13
                                 || 12 
                                 7|    
                                  9    


Chain C from PDB  Type:RNA  Length:17
                                                
                  1zft C 15 GGCAGAGAAACACACGA 31
                                    24       


Chain D from PDB  Type:RNA  Length:19
                                                  
                  1zft D 31 UCGUGGUACAUUACCUGCC 49
                                    40
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 Classification and Annotation

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 Related Entries

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(-) Related Entries Specified in the PDB File

1x9c THE CRYSTAL STRUCTURE OF AN ALL-RNA MINIMAL HAIRPIN RIBOZYME (G8, U39C, LOW SALT CONDITIONS)
1x9k THE CRYSTAL STRUCTURE OF AN ALL-RNA MINIMAL HAIRPIN RIBOZYME (G8, U39C, HIGH SALT CONDITIONS)
1zfr AN ALL-RNA HAIRPIN RIBOZYME WITH MUTATION U39C AND 2MA AT A -1(LOW SALT)
1zfv AN ALL-RNA HAIRPIN RIBOZYME WITH MUTATIONS G8A, U39C AND 2' -OH AT A-1 (LOW SALT)
1zfx ALL-RNA HAIRPIN RIBOZYME WITH MUTATIONS G8U AND U39C (LOW SALT)