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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HAIPRIN RIBOZYME WITH A 2',5'-LINKED SUBSTRATE AND N1-DEAZAADENOSINE AT POSITION A10
 
Authors :  J. E. Wedekind, R. C. Spitale, J. Krucinska
Date :  29 Jun 09  (Deposition) - 03 Nov 09  (Release) - 03 Nov 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Hairpin Ribozyme, N1-Deazaadenosine, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. C. Spitale, R. Volpini, M. V. Mungillo, J. Krucinska, G. Cristalli, J. E. Wedekind
Single-Atom Imino Substitutions At A9 And A10 Reveal Distinct Effects On The Fold And Function Of The Hairpin Ribozyme Catalytic Core.
Biochemistry V. 48 7777 2009
PubMed-ID: 19634899  |  Reference-DOI: 10.1021/BI9011622
(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*GP*U)- 3'
    Chains: A
    Engineered: YES
    Other Details: HAIRPIN RIBOZYME
    Other Details - Source: THE RNA WAS SYNTHESIZED BY DHARMACON INC., FOLLOWING THE TOBACCO RINGSPOT VIRUS SEQUENCE
    Synthetic: YES
 
Molecule 2 - DNA/RNA (30-MER)
    Chains: B
    Engineered: YES
    Other Details: HAIRPIN RIBOZYME
    Other Details - Source: THE RNA WAS SYNTHESIZED BY DHARMACON INC., FOLLOWING THE TOBACCO RINGSPOT VIRUS SEQUENCE
    Synthetic: YES
 
Molecule 3 - 5'- R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C) -3'
    Chains: C
    Engineered: YES
    Other Details: HAIRPIN RIBOZYME
    Other Details - Source: THE RNA WAS SYNTHESIZED BY DHARMACON INC., FOLLOWING THE TOBACCO RINGSPOT VIRUS SEQUENCE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
11DP1Mod. NucleotideN1-DEAZA-ADENOSINE-5'-MONOPHOSPHATE
2NCO2Ligand/IonCOBALT HEXAMMINE(III)
3S9L1Mod. Nucleotide2-[2-(2-HYDROXYETHOXY)ETHOXY]ETHYL DIHYDROGEN PHOSPHATE
4SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREA B:20 , G B:21 , A C:40 , U C:41BINDING SITE FOR RESIDUE NCO B 101
2AC2SOFTWAREC A:2 , SO4 A:103 , G B:11 , G B:12 , G B:13BINDING SITE FOR RESIDUE NCO B 102
3AC3SOFTWAREU A:1 , C A:2 , NCO B:102BINDING SITE FOR RESIDUE SO4 A 103

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3I2U)

(-) 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)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:RNA  Length:13
                                            
                  3i2u A  1 UCCCAGUCCACCG 13
                                    10   


Chain B from PDB  Type:DNA/RNA  Length:30
                                                             
                  3i2u B  2 CGGUGAGAxGGGxGGCAGAGAAACACACGA 31
                                    11  |     21        31
                                   10-1DP                 
                                       14-S9L             


Chain C from PDB  Type:RNA  Length:19
                                                  
                  3i2u C 31 UCGUGGUACAUUACCUGCC 49
                                    40
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 Classification and Annotation

(-) SCOP 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

3i2p CRYSTAL STRUCTURE OF THE HAIRPIN RIBOZYME PRODUCT-MIMIC WITH 5'-DEOXY-5'-FLUOROGUANOSINE
3i2q CRYSTAL STRUCTURE OF THE HAIRPIN RIBOZYME WITH 2'OME SUBSTRATE STRAND AND N1-DEAZAADENOSINE AT POSITION A9
3i2r CRYSTAL STRUCTURE OF THE HAIRPIN RIBOZYME WITH A 2',5'- LINKED SUBSTRATE WITH N1-DEAZAADENOSINE AT POSITION A9
3i2s CRYSTAL STRUCTURE OF THE HAIRPIN RIBOZYME WITH A 2'OME SUBSTRATE AND N1-DEAZAADENOSINE AT POSITION A10