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(-) Description

Title :  CRYSTAL STRUCTURE OF THE 2'- DEOXYGUANOSINE RIBOSWITCH BOUND TO 2'-DEOXYGUANOSINE, CESIUM SOAK
 
Authors :  O. Pikovskaya, A. Polonskaia, D. J. Patel, A. Serganov
Date :  23 Jun 11  (Deposition) - 17 Aug 11  (Release) - 26 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Three-Way Rna Junction, Riboswitch, 2'-Deoxy Guanosine, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Pikovskaya, A. Polonskaia, D. J. Patel, A. Serganov
Structural Principles Of Nucleoside Selectivity In A 2'-Deoxyguanosine Riboswitch.
Nat. Chem. Biol. V. 7 748 2011
PubMed-ID: 21841796  |  Reference-DOI: 10.1038/NCHEMBIO.631

(-) Compounds

Molecule 1 - RNA (66-MER)
    Chains: A, B
    Engineered: YES
    Other Details: DG RIBOSWITCH (66-MER)
    Other Details - Source: IN VITRO TRANSCRIBED RNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 14)

Asymmetric Unit (5, 14)
No.NameCountTypeFull Name
1CCC2Mod. NucleotideCYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
2CS6Ligand/IonCESIUM ION
3GNG2Ligand/Ion2'-DEOXY-GUANOSINE
4GTP2Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
5MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1CCC1Mod. NucleotideCYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
2CS-1Ligand/IonCESIUM ION
3GNG1Ligand/Ion2'-DEOXY-GUANOSINE
4GTP1Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
5MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1CCC1Mod. NucleotideCYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
2CS-1Ligand/IonCESIUM ION
3GNG1Ligand/Ion2'-DEOXY-GUANOSINE
4GTP1Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
5MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREA A:30 , C A:31 , C A:56 , C A:57 , C A:58 , G A:59 , C A:80 , U A:81 , CS A:202BINDING SITE FOR RESIDUE GNG A 120
2AC2SOFTWAREG A:46 , G A:47 , A A:71 , U A:72BINDING SITE FOR RESIDUE CS A 201
3AC3SOFTWAREC A:31 , A A:32 , GNG A:120BINDING SITE FOR RESIDUE CS A 202
4AC4SOFTWAREG A:33 , G A:34 , G A:35BINDING SITE FOR RESIDUE CS A 203
5AC5SOFTWAREG A:38 , C A:39 , G A:47 , C A:48 , A A:66 , A A:67BINDING SITE FOR RESIDUE CS A 204
6AC6SOFTWAREC A:68 , U A:72BINDING SITE FOR RESIDUE CS A 205
7AC7SOFTWAREG A:45 , G A:46BINDING SITE FOR RESIDUE MG A 206
8AC8SOFTWAREU A:63 , G A:75 , G A:76BINDING SITE FOR RESIDUE MG A 305
9AC9SOFTWAREA B:30 , C B:31 , C B:56 , C B:57 , C B:58 , G B:59 , C B:80 , U B:81 , HOH B:307BINDING SITE FOR RESIDUE GNG B 120

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3SKW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SKW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3SKW)

(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  UniProt sequence: complete  aligned part    
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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:66
                                                                                                 
                  3skw A 23 gGCUUAUACAGGGUAGCAUAAUGGGCUACUGACCCCGCCUUCAAACCUAUUUGGAGACUAUAAGUc 88
                            |       32        42        52        62        72        82     |
                            |                                                               88-CCC
                           23-GTP                                                             


Chain B from PDB  Type:RNA  Length:66
                                                                                                 
                  3skw B 23 gGCUUAUACAGGGUAGCAUAAUGGGCUACUGACCCCGCCUUCAAACCUAUUUGGAGACUAUAAGUc 88
                            |       32        42        52        62        72        82     |
                            |                                                               88-CCC
                           23-GTP
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  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 3SKW)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3SKW)

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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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

3ski 3skl 3skr 3skt 3skz