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(-) Description

Title :  CRYSTAL STRUCTURE OF A JUNCTIONED HAIRPIN RIBOZYME INCORPORATING 9ATOM LINKER AND 2'-DEOXY 2'-AMINO U AT A-1
 
Authors :  C. Macelrevey, J. Krucinska, J. E. Wedekind
Date :  30 Oct 06  (Deposition) - 14 Aug 07  (Release) - 17 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hairpin Ribozyme, Mutation, S-Turn, E-Loop, Ribose Zipper, Catalytic Rna, 2'-Deoxy 2'-Amino, 9S Linker, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Macelrevey, R. C. Spitale, J. Krucinska, J. E. Wedekind
A Posteriori Design Of Crystal Contacts To Improve The X-Ra Diffraction Properties Of A Small Rna Enzyme.
Acta Crystallogr. , Sect. D V. 63 812 2007
PubMed-ID: 17582172  |  Reference-DOI: 10.1107/S090744490702464X

(-) Compounds

Molecule 1 - 5'-R(*UP*CP*CP*CP*(U2N)P*GP*UP*CP*CP*AP*CP*CP*G)-3'
    Chains: A
    Engineered: YES
    Other Details: RIBOZYME SUBSTRATE STRAND
    Other Details - Source: SEQUENCE OCCURS NATURALLY IN SATELLITE RNA TOBACCO RINGSPOT VIRUS
    Synthetic: YES
 
Molecule 2 - 5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3'
    Chains: B
    Engineered: YES
    Other Details: RIBOZYME DOMAIN LINKING STRAND
    Other Details - Source: SEQUENCE OCCURS NATURALLY IN SATELLITE RNA 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
    Fragment: S-TURN STRAND
    Mutation: YES
    Other Details: RIBOZYME DOMAIN LINKING STRAND
    Other Details - Source: SEQUENCE OCCURS NATURALLY IN SATELLITE RNA 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
    Other Details: RIBOZYME S-TURN STRAND
    Other Details - Source: SEQUENCE OCCURS NATURALLY IN SATELLITE RNA 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, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
12AU1Mod. Nucleotide2'-AMINOURIDINE
2NCO1Ligand/IonCOBALT HEXAMMINE(III)
3S9L1Ligand/Ion2-[2-(2-HYDROXYETHOXY)ETHOXY]ETHYL DIHYDROGEN PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREA C:20 , G C:21 , A D:40 , U D:41BINDING SITE FOR RESIDUE NCO C 32
2AC2SOFTWAREU A:1 , G B:13 , G C:15BINDING SITE FOR RESIDUE S9L C 14

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2NPY)

(-) 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:DNA/RNA  Length:13
                                            
                  2npy A  1 UCCCuGUCCACCG 13
                                |   10   
                                |        
                                5-2AU    


Chain B from PDB  Type:RNA  Length:12
                                           
                  2npy B  2 CGGUGAGAAGGG 13
                                    11  


Chain C from PDB  Type:RNA  Length:17
                                                
                  2npy C 15 GGCAGAGAAACACACGA 31
                                    24       


Chain D from PDB  Type:RNA  Length:19
                                                  
                  2npy D 31 UCGUGGUACAUUACCUGCC 49
                                    40
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

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(-) CATH Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

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 Related Entries

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(-) Related Entries Specified in the PDB File

1zfr 2.05 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF JUNCTIONLESS HAIRPIN RIBOZYME
2npz