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(-) Description

Title :  THE STRUCTURE OF THE E.COLI GUANIDINE II RIBOSWITCH P1 STEM-LOOP
 
Authors :  L. Huang, J. Wang, D. M. J. Lilley
Date :  08 Mar 17  (Deposition) - 31 May 17  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.57
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Guanidine Ii Riboswitch, Stem-Loop, Tetra Loop, Dimer, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Huang, J. Wang, D. M. J. Lilley
The Structure Of The Guanidine-Ii Riboswitch.
Cell Chem Biol V. 24 695 2017
PubMed-ID: 28529131  |  Reference-DOI: 10.1016/J.CHEMBIOL.2017.05.014

(-) Compounds

Molecule 1 - RNA (5'- R(*UP*UP*UP*GP*CP*AP*GP*GP*AP*CP*GP*AP*CP*CP*UP*GP*(CBV)P*AP*AP*A)- 3')
    ChainsA, B, C, D
    EngineeredYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1CBV4Mod. Nucleotide5-BROMOCYTIDINE 5'-(DIHYDROGEN PHOSPHATE)
2GAI4Ligand/IonGUANIDINE
3NA1Ligand/IonSODIUM ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CBV2Mod. Nucleotide5-BROMOCYTIDINE 5'-(DIHYDROGEN PHOSPHATE)
2GAI2Ligand/IonGUANIDINE
3NA-1Ligand/IonSODIUM ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1CBV2Mod. Nucleotide5-BROMOCYTIDINE 5'-(DIHYDROGEN PHOSPHATE)
2GAI2Ligand/IonGUANIDINE
3NA-1Ligand/IonSODIUM ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREG A:8 , A A:9 , C A:10 , G A:11binding site for residue GAI A 101
02AC2SOFTWAREG B:8 , A B:9 , C B:10 , G B:11binding site for residue GAI B 101
03AC3SOFTWAREG B:8binding site for residue NA B 102
04AC4SOFTWAREG C:8 , A C:9 , C C:10 , G C:11binding site for residue GAI C 101
05AC5SOFTWAREG D:8 , A D:9 , C D:10 , G D:11binding site for residue GAI D 101
06AC6SOFTWAREG A:7 , G A:8 , G B:4 , C B:5 , A B:6 , U B:15 , A B:18 , HOH B:202 , HOH B:203binding site for Di-nucleotide G B 16 and CBV B 17
07AC7SOFTWAREG A:8 , U B:3 , G B:4 , G B:16 , A B:19 , HOH B:202 , HOH B:203binding site for Di-nucleotide CBV B 17 and A B 18
08AC8SOFTWAREG C:4 , C C:5 , A C:6 , U C:15 , A C:18 , G D:7 , G D:8binding site for Di-nucleotide G C 16 and CBV C 17
09AC9SOFTWAREU C:3 , G C:4 , C C:5 , G C:16 , A C:19 , G D:8binding site for Di-nucleotide CBV C 17 and A C 18
10AD1SOFTWAREG C:8 , G D:4 , C D:5 , A D:6 , U D:15 , A D:18binding site for Di-nucleotide G D 16 and CBV D 17
11AD2SOFTWAREU B:2 , G C:8 , U D:3 , G D:4 , C D:5 , G D:16 , A D:19binding site for Di-nucleotide CBV D 17 and A D 18

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5NDI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5NDI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 5NDI)

(-) 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    
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Chain A from PDB  Type:RNA  Length:20
                                                   
                  5ndi A  1 UUUGCAGGACGACCUGxAAA 20
                                    10      | 20
                                           17-CBV

Chain B from PDB  Type:RNA  Length:20
                                                   
                  5ndi B  1 UUUGCAGGACGACCUGxAAA 20
                                    10      | 20
                                           17-CBV

Chain C from PDB  Type:RNA  Length:20
                                                   
                  5ndi C  1 UUUGCAGGACGACCUGxAAA 20
                                    10      | 20
                                           17-CBV

Chain D from PDB  Type:RNA  Length:20
                                                   
                  5ndi D  1 UUUGCAGGACGACCUGxAAA 20
                                    10      | 20
                                           17-CBV

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 Classification and Annotation

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(-) Gene Ontology  (0, 0)

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