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(-) Description

Title :  STRUCTURE OF THE TETRAHYMENA RIBOZYME: BASE TRIPLE SANDWICH AND METAL ION AT THE ACTIVE SITE
 
Authors :  F. Guo, A. R. Gooding, T. R. Cech
Date :  18 Aug 04  (Deposition) - 09 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Catalytic Rna, Ribozyme, Group I Intron, Crystal Structure, Guanosine Binding Site, Metal Ions, Active Site, Catalytic Mechanism, Base Triples, Conformational Changes (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Guo, A. R. Gooding, T. R. Cech
Structure Of The Tetrahymena Ribozyme: Base Triple Sandwich And Metal Ion At The Active Site.
Mol. Cell V. 16 351 2004
PubMed-ID: 15525509  |  Reference-DOI: 10.1016/J.MOLCEL.2004.10.003
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TETRAHYMENA RIBOZYME RNA
    Chains: A, B, C, D
    Engineered: YES
    Mutation: YES
    Other Details: GROUP I INTRON IN LARGE RIBOSOMAL RNA SUBUNIT
    Other Details - Source: RNA WAS PREPARED BY IN VITRO TRANSCRIPTION. THE SEQUENCE OF THIS RNA CAN BE FOUND NATURALLY IN TETRAHYMENA THERMOPHILA.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 38)

Asymmetric Unit (1, 38)
No.NameCountTypeFull Name
1MG38Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (31, 31)

Asymmetric Unit (31, 31)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREA C:184 , A C:186 , A C:187 , G C:188BINDING SITE FOR RESIDUE MG C 1
02AC2SOFTWAREA B:183 , A B:184 , A B:186 , A B:187 , G B:188BINDING SITE FOR RESIDUE MG B 2
03AC3SOFTWAREA A:183 , A A:184 , A A:186 , A A:187 , G A:188BINDING SITE FOR RESIDUE MG A 3
04AC4SOFTWAREA D:184 , A D:186 , A D:187 , G D:188BINDING SITE FOR RESIDUE MG D 4
05AC5SOFTWAREA B:256 , U B:273 , C B:274BINDING SITE FOR RESIDUE MG B 5
06AC6SOFTWAREC B:209 , G B:210BINDING SITE FOR RESIDUE MG B 6
07AC7SOFTWAREC C:208 , C C:262 , A C:306 , G C:414BINDING SITE FOR RESIDUE MG C 7
08AC8SOFTWAREA D:256 , U D:273 , C D:274BINDING SITE FOR RESIDUE MG D 8
09AC9SOFTWAREC A:209 , G A:210 , G A:303BINDING SITE FOR RESIDUE MG A 9
10BC1SOFTWAREA C:256 , U C:273BINDING SITE FOR RESIDUE MG C 10
11BC2SOFTWAREMG A:2 , A A:173BINDING SITE FOR RESIDUE MG A 11
12BC3SOFTWAREU D:249 , G D:250BINDING SITE FOR RESIDUE MG D 12
13BC4SOFTWAREA B:172 , A B:173BINDING SITE FOR RESIDUE MG B 13
14BC5SOFTWAREC A:255 , A A:256 , U A:273BINDING SITE FOR RESIDUE MG A 14
15BC6SOFTWAREA D:173BINDING SITE FOR RESIDUE MG D 15
16BC7SOFTWAREC B:262 , U B:305 , A B:306 , G B:414BINDING SITE FOR RESIDUE MG B 16
17BC8SOFTWAREC A:262 , U A:305 , A A:306 , G A:414BINDING SITE FOR RESIDUE MG A 17
18BC9SOFTWAREU C:249 , G C:250BINDING SITE FOR RESIDUE MG C 18
19CC1SOFTWAREC D:209 , G D:210BINDING SITE FOR RESIDUE MG D 19
20CC2SOFTWAREA C:172 , A C:173BINDING SITE FOR RESIDUE MG C 20
21CC3SOFTWAREA B:248 , U B:249 , G B:250BINDING SITE FOR RESIDUE MG B 21
22CC4SOFTWAREG D:304 , U D:305 , A D:306 , G D:414BINDING SITE FOR RESIDUE MG D 22
23CC5SOFTWAREMG A:11BINDING SITE FOR RESIDUE MG A 2
24CC6SOFTWAREG B:147BINDING SITE FOR RESIDUE MG B 3
25CC7SOFTWAREG D:147BINDING SITE FOR RESIDUE MG D 415
26CC8SOFTWAREG B:174 , G B:176BINDING SITE FOR RESIDUE MG B 415
27CC9SOFTWAREG C:147 , G C:148BINDING SITE FOR RESIDUE MG C 6
28DC1SOFTWAREU A:202BINDING SITE FOR RESIDUE MG A 7
29DC2SOFTWAREG C:118 , G C:119 , G C:201BINDING SITE FOR RESIDUE MG C 415
30DC3SOFTWAREG C:174BINDING SITE FOR RESIDUE MG C 11
31DC4SOFTWAREG D:281BINDING SITE FOR RESIDUE MG D 417

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X8W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1X8W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X8W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1X8W)

(-) Exons   (0, 0)

(no "Exon" information available for 1X8W)

(-) Sequences/Alignments

Asymmetric 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    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:RNA  Length:242
                                                                                                                                                                                                                                                                                  
                 1x8w A  96 GACCGUCAAAUUGCGGGAAAGGGGUCAACAGCCGUUCAGUACCAAGUCUCAGGGGAAACUUUGAGAUGGCCUUGCAAAGGGUAUGGUAAUAAGCUGACGGACAUGGUCCUAACCGCGCAGCCAAGUCCUAAGUCAACAGGAGACUGUUGAUAUGGAUGCAGUACACAGACUAGAUGUCGGCCGGGGAAGAUCUUCUCAUAAGGUAUAGUCGGACCUCUCCCGAAAGGGAGUUGGAGUACUCG 414
                                   105       115       125       135       145       155       165       175       185       195       205       215       225       235  ||   246       256       266       276       286|      301       311       321       331|      412  
                                                                                                                                                                        238|                                           286|                                    331|           
                                                                                                                                                                         240                                            292                                     403           


Chain B from PDB  Type:RNA  Length:247
                                                                                                                                                                                                                                                                                       
                 1x8w B  96 GACCGUCAAAUUGCGGGAAAGGGGUCAACAGCCGUUCAGUACCAAGUCUCAGGGGAAACUUUGAGAUGGCCUUGCAAAGGGUAUGGUAAUAAGCUGACGGACAUGGUCCUAACCGCGCAGCCAAGUCCUAAGUCAACAGGAGACUGUUGAUAUGGAUGCAGUACACAGACUAGAUGUCGGCCGGGGAAGAUGUAUUCUUCUCAUAAGGUAUAGUCGGACCUCUCCCGAAAGGGAGUUGGAGUACUCG 414
                                   105       115       125       135       145       155       165       175       185       195       205       215       225       235  ||   246       256       266       276       286       296       306       316       326    || 407       
                                                                                                                                                                        238|                                                                                        331|           
                                                                                                                                                                         240                                                                                         403           


Chain C from PDB  Type:RNA  Length:237
                                                                                                                                                                                                                                                                             
                 1x8w C  96 GACCGUCAAAUUGCGGGAAAGGGGUCAACAGCCGUUCAGUACCAAGUCUCAGGGGAAACUUUGAGAUGGCCUUGCAAAGGGUAUGGUAAUAAGCUGACGGACAUGGUCCUAACCGCGCAGCCAAGUCCUAAGUCAACAGGAGACUGUUGAUAUGGAUGCAGUACACAGACUAGAUGUCGGCCGGGGAAGAUCUUCUCAUAAGGUAUAGUCGGACCUCUCCCGAAAGGGAGUUGGUCG 414
                                   105       115       125       135       145       155       165       175       185       195       205       215       225       235  ||   246       256       266       276       286|      301       311       321       331|  ||  
                                                                                                                                                                        238|                                           286|                                    331|  ||  
                                                                                                                                                                         240                                            292                                     403  ||  
                                                                                                                                                                                                                                                                   406|  
                                                                                                                                                                                                                                                                    412  


Chain D from PDB  Type:RNA  Length:242
                                                                                                                                                                                                                                                                                  
                 1x8w D  96 GACCGUCAAAUUGCGGGAAAGGGGUCAACAGCCGUUCAGUACCAAGUCUCAGGGGAAACUUUGAGAUGGCCUUGCAAAGGGUAUGGUAAUAAGCUGACGGACAUGGUCCUAACCGCGCAGCCAAGUCCUAAGUCAACAGGAGACUGUUGAUAUGGAUGCAGUACACAGACUAGAUGUCGGCCGGGGAAGAUCUUCUCAUAAGGUAUAGUCGGACCUCUCCCGAAAGGGAGUUGGAGUACUCG 414
                                   105       115       125       135       145       155       165       175       185       195       205       215       225       235  ||   246       256       266       276       286|      301       311       321       331|      412  
                                                                                                                                                                        238|                                           286|                                    331|           
                                                                                                                                                                         240                                            292                                     403
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 1X8W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1X8W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1X8W)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1X8W)

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