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(-) Description

Title :  CRYSTAL STRUCTURE OF A MINIMAL, NATIVE (U39) ALL-RNA HAIRPIN RIBOZYME
 
Authors :  S. Alam, V. Grum-Tokars, J. Krucinska, M. L. Kundracik, J. E. Wedekind
Date :  11 Sep 05  (Deposition) - 01 Nov 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Ribozyme, S-Turn, Dual Conformation, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Alam, V. Grum-Tokars, J. Krucinska, M. L. Kundracik, J. E. Wedekind
Conformational Heterogeneity At Position U37 Of An All-Rna Hairpin Ribozyme With Implications For Metal Binding And Th Catalytic Structure Of The S-Turn
Biochemistry V. 44 14396 2005
PubMed-ID: 16262240  |  Reference-DOI: 10.1021/BI051550I
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-R(*UP*CP*CP*CP*(A2M)P*GP*UP*CP*CP*AP*CP*CP*G)-3'
    Chains: A
    Engineered: YES
    Synonym: RIBOZYME
    Synthetic: YES
 
Molecule 2 - 5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3'
    Chains: B
    Engineered: YES
    Synonym: RIBOZYME
    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
    Synonym: RIBOZYME
    Synthetic: YES
 
Molecule 4 - 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*UP*AP*UP*UP*AP*CP*CP*UP*GP*CP *C)-3'
    Chains: D
    Engineered: YES
    Synonym: RIBOZYME
    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:2BINDING SITE FOR RESIDUE SO4 A 201
2AC2SOFTWAREG C:19 , A C:20 , G C:21 , A D:40 , U D:41BINDING SITE FOR RESIDUE NCO C 101
3AC3SOFTWAREU A:7 , A B:9 , A B:10 , A C:26 , C C:27BINDING SITE FOR RESIDUE NCO B 102

(-) SS Bonds  (0, 0)

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(-) 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
   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
                                            
                  2d2k A  1 UCCCaGUCCACCG 13
                                |   10   
                                |        
                                5-A2M    


Chain B from PDB  Type:RNA  Length:12
                                           
                  2d2k B  2 CGGUGAGAAGGG 13
                                    11  


Chain C from PDB  Type:RNA  Length:17
                                                
                  2d2k C 15 GGCAGAGAAACACACGA 31
                                    24       


Chain D from PDB  Type:RNA  Length:19
                                                  
                  2d2k D 31 UCGUGGUAUAUUACCUGCC 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

1x9c MINIMAL HAIRPIN RIBOZYME WITH MUTATION U39C
1x9k HIGH-SALT MINIMAL HAIRPIN RIBOZYME
2d2l MINIMAL ALL-RNA HAIRPIN RIBOZYME WITH A PROPYL LINKER (C3) AT POSITION U39