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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HAIRPIN RIBOZYME WITH 2'OME SUBSTRATE STRAND AND N1-DEAZAADENOSINE AT POSITION A9
 
Authors :  J. E. Wedekind, R. C. Spitale, J. Krucinska
Date :  29 Jun 09  (Deposition) - 03 Nov 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
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

(-) Compounds

Molecule 1 - 5'-R(*UP*CP*CP*CP*(A2M)P*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  (5, 5)

Asymmetric/Biological Unit (5, 5)
No.NameCountTypeFull Name
11DP1Mod. NucleotideN1-DEAZA-ADENOSINE-5'-MONOPHOSPHATE
2A2M1Mod. Nucleotide2'-O-METHYLADENOSINE 5'-(DIHYDROGEN PHOSPHATE)
3NCO1Ligand/IonCOBALT HEXAMMINE(III)
4S9L1Mod. Nucleotide2-[2-(2-HYDROXYETHOXY)ETHOXY]ETHYL DIHYDROGEN PHOSPHATE
5SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREU A:-5 , C A:-4 , SO4 A:102 , G B:11 , G B:12 , G B:13 , A B:20 , G B:21 , A C:40 , U C:41BINDING SITE FOR RESIDUE NCO B 101
2AC2SOFTWAREU A:-5 , C A:-4 , NCO B:101BINDING SITE FOR RESIDUE SO4 A 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3I2Q)

(-) 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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Chain A from PDB  Type:RNA  Length:13
                                            
                  3i2q A -5 UCCCaGUCCACCG  8
                                ||   5   
                                ||       
                               -1-A2M    
                                 1       


Chain B from PDB  Type:DNA/RNA  Length:30
                                                             
                  3i2q B  2 CGGUGAGxAGGGxGGCAGAGAAACACACGA 31
                                   |11  |     21        31
                                   9-1DP|                 
                                       14-S9L             


Chain C from PDB  Type:RNA  Length:19
                                                  
                  3i2q C 31 UCGUGGUACAUUACCUGCC 49
                                    40
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3I2Q)

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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
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
3i2u CRYSTAL STRUCTURE OF THE HAIPRIN RIBOZYME WITH A 2',5'- LINKED SUBSTRATE AND N1-DEAZAADENOSINE AT POSITION A10