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(-) Description

Title :  CRYSTAL STRUCTURE OF A JUNCTIONLESS ALL-RNA HAIRPIN RIBOZYME AT 2.05 ANGSTROMS RESOLUTION
 
Authors :  J. E. Wedekind
Date :  10 Feb 07  (Deposition) - 06 Mar 07  (Release) - 17 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Rna, Hairpin Ribozyme, All-Rna, 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

(-) Compounds

Molecule 1 - SUBSTRATE STRAND - MINIMAL JUNCTIONLESS HAIRPIN RIBOZYME
    Chains: A
    Engineered: YES
    Other Details: CHEMICALLY SYNTHESIZED BASED ON SATELLITE TOBACCO RINGSPOT VIRUS
    Synthetic: YES
 
Molecule 2 - LOOP A RIBOZYME STRAND
    Chains: B
    Engineered: YES
    Other Details: CHEMICALLY SYNTHESIZED BASED ON SATELLITE TOBACCO RINGSPOT VIRUS
    Synthetic: YES
 
Molecule 3 - LOOP B RIBOZYME STRAND
    Chains: C
    Engineered: YES
    Other Details: CHEMICALLY SYNTHESIZED BASED ON SATELLITE TOBACCO RINGSPOT VIRUS
    Synthetic: YES
 
Molecule 4 - LOOP B S-TURN STRAND
    Chains: D
    Engineered: YES
    Other Details: CHEMICALLY SYNTHESIZED BASED ON 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:-4 , U A:-5 , NCO B:101BINDING SITE FOR RESIDUE SO4 A 201
2AC2SOFTWAREC A:-4 , SO4 A:201 , G B:11 , G B:12 , G B:13BINDING SITE FOR RESIDUE NCO B 101
3AC3SOFTWAREA C:20 , G C:21 , A D:40 , U D:41BINDING SITE FOR RESIDUE NCO D 101

(-) SS Bonds  (0, 0)

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

(-) 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
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Chain A from PDB  Type:RNA  Length:13
                                            
                  2oue A -5 UCCCaGUCCACCG  8
                                ||   5   
                                ||       
                               -1-A2M    
                                 1       


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


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


Chain D from PDB  Type:RNA  Length:19
                                                  
                  2oue D 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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  2oue
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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 MINIMAL HAIRPIN RIBOZYME, A2M AT A-1, U39C MUTANT (LOW SALT)
1x9k MINIMAL HAIRPIN RIBOZYME, A2M AT A-1, U39C MUTANT (HIGH 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)
1zfx ALL-RNA HAIRPIN RIBOZYME WITH MUTATIONS G8U AND U39C (LOW SALT)
2bcy MINIMAL HAIRPIN RIBOZYME, 2'-OH AT A-1, G82AP AND U39C MUTATIONS (LOW SALT)
2bcz MINIMAL HAIRPIN RIBOZYME, A2M AT A-1, G8I AND U39C MUTATIONS (LOW SALT)
2fgp MINIMAL HAIRPIN RIBOZYME, 2'-OH AT A-1, G8DAP AND U39C MUTATIONS (LOW SALT)