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(-) Description

Title :  THE STRUCTURE OF A MINIMAL ALL-RNA HAIRPIN RIBOZYME WITH THE MUTANT G8U AT THE CLEAVAGE SITE
 
Authors :  J. E. Wedekind
Date :  20 Apr 05  (Deposition) - 14 Feb 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.38
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hairpin Ribozyme, All-Rna, Cobalt Hexaamine, Mutation, Low Salt, S-Turn, E-Loop, Ribose Zipper, Catalytic 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*AP*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*UP*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
    Mutation: 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  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1NCO2Ligand/IonCOBALT HEXAMMINE(III)
2SO41Ligand/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:12 , G B:13 , HOH B:105BINDING SITE FOR RESIDUE NCO B 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZFX)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (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)
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Chain A from PDB  Type:RNA  Length:13
                                            
                  1zfx A  1 UCCCAGUCCACCG 13
                                    10   


Chain B from PDB  Type:RNA  Length:12
                                           
                  1zfx B  2 CGGUGAUAAGGG 13
                                    11  


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


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

(-) SCOP Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

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  1zfx
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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

1x9c AN ALL-RNA HAIRPIN RIBOZYME WITH MUTATION U39C (LOW SALT)
1x9k AN ALL-RNA HAIRPIN RIBOZYME WITH MUTATION U39C AND 2MA AT A -1 (HIGH SALT)
1zfr AN ALL-RNA HAIRPIN RIBOZYME WITH MUTATION U39C AND 2MA AT A -1(LOW SALT)
1zft AN ALL-RNA HAIRPIN RIBOZYME WITH MUTATIONS G8I, 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)