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(-) Description

Title :  BASE PAIRING AND STRUCTURE INSIGHTS INTO THE 5-FORMYLCYTOSINE IN RNA DUPLEX
 
Authors :  Z. P. Luo, J. Sheng
Date :  18 Jan 16  (Deposition) - 27 Apr 16  (Release) - 15 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.24
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  Rna, 5-Formylcytosine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Wang, Z. Luo, K. He, M. O. Delaney, D. Chen, J. Sheng
Base Pairing And Structural Insights Into The 5-Formylcytosine In Rna Duplex.
Nucleic Acids Res. V. 44 4968 2016
PubMed-ID: 27079978  |  Reference-DOI: 10.1093/NAR/GKW235

(-) Compounds

Molecule 1 - RNA (5'-R(*GP*UP*AP*(OFC)P*GP*UP*AP*C)-3')
    Chains: A, B, C, D, E, F
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB    
Biological Unit 2 (1x):   CD  
Biological Unit 3 (1x):     EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1NA2Ligand/IonSODIUM ION
2RSQ6Mod. Nucleotide5-FORMYLCYTIDINE 5'-(DIHYDROGEN PHOSPHATE)
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
2RSQ2Mod. Nucleotide5-FORMYLCYTIDINE 5'-(DIHYDROGEN PHOSPHATE)
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
2RSQ2Mod. Nucleotide5-FORMYLCYTIDINE 5'-(DIHYDROGEN PHOSPHATE)
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
2RSQ2Mod. Nucleotide5-FORMYLCYTIDINE 5'-(DIHYDROGEN PHOSPHATE)

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:236 , HOH C:112 , HOH C:115 , HOH C:117 , HOH C:139 , HOH D:142binding site for residue NA A 101
02AC2SOFTWAREHOH A:235 , HOH A:241 , HOH B:205 , HOH B:211 , HOH B:215 , HOH D:135binding site for residue NA B 101
03AC3SOFTWAREG A:5 , U A:6 , A A:7 , U B:2 , G B:5 , HOH B:201 , HOH B:202 , HOH B:204 , HOH B:210 , HOH B:214 , HOH B:217 , HOH B:219 , HOH B:224 , HOH B:225 , A F:3 , HOH F:102 , HOH F:112 , HOH F:128 , HOH F:143binding site for Di-nucleotide A B 3 and RSQ B 4
04AC4SOFTWAREA A:3 , RSQ A:4 , G A:5 , U A:6 , A B:3 , U B:6 , HOH B:201 , HOH B:206 , HOH B:212 , HOH B:217 , HOH B:218 , HOH B:221 , HOH B:222 , HOH B:224 , HOH B:229 , A F:3 , HOH F:102 , HOH F:128 , HOH F:143binding site for Di-nucleotide RSQ B 4 and G B 5
05AC5SOFTWAREU C:2 , G C:5 , HOH C:101 , HOH C:103 , HOH C:107 , HOH C:113 , HOH C:114 , HOH C:122 , HOH C:126 , HOH C:128 , HOH C:131 , G D:5 , U D:6 , A D:7 , HOH E:118binding site for Di-nucleotide A C 3 and RSQ C 4
06AC6SOFTWAREA C:3 , U C:6 , HOH C:101 , HOH C:107 , HOH C:116 , HOH C:120 , HOH C:121 , HOH C:123 , HOH C:126 , HOH C:127 , HOH C:131 , A D:3 , RSQ D:4 , G D:5 , U D:6 , HOH E:118 , HOH E:131binding site for Di-nucleotide RSQ C 4 and G C 5
07AC7SOFTWAREG C:5 , U C:6 , A C:7 , U D:2 , G D:5 , HOH D:104 , HOH D:116 , HOH D:117 , HOH D:118 , HOH D:127 , HOH D:128 , HOH D:130 , HOH D:136binding site for Di-nucleotide A D 3 and RSQ D 4
08AC8SOFTWARERSQ C:4 , G C:5 , A D:3 , U D:6 , HOH D:104 , HOH D:105 , HOH D:106 , HOH D:109 , HOH D:111 , HOH D:119 , HOH D:121 , HOH D:127 , HOH D:130 , HOH D:133 , HOH D:134binding site for Di-nucleotide RSQ D 4 and G D 5
09AC9SOFTWAREU E:2 , G E:5 , HOH E:102 , HOH E:104 , HOH E:111 , HOH E:114 , HOH E:118 , HOH E:119 , HOH E:131 , HOH E:135 , HOH E:136 , HOH E:137 , G F:5 , U F:6 , A F:7 , HOH F:136 , HOH F:144binding site for Di-nucleotide A E 3 and RSQ E 4
10AD1SOFTWAREA E:3 , U E:6 , HOH E:102 , HOH E:104 , HOH E:106 , HOH E:119 , HOH E:120 , HOH E:121 , HOH E:128 , HOH E:131 , HOH E:133 , HOH E:136 , HOH E:137 , A F:3 , RSQ F:4 , G F:5 , HOH F:136 , HOH F:144binding site for Di-nucleotide RSQ E 4 and G E 5
11AD2SOFTWARERSQ B:4 , G E:5 , U E:6 , A E:7 , U F:2 , G F:5 , HOH F:102 , HOH F:103 , HOH F:105 , HOH F:106 , HOH F:109 , HOH F:112 , HOH F:115 , HOH F:123 , HOH F:124 , HOH F:130 , HOH F:133 , HOH F:135binding site for Di-nucleotide A F 3 and RSQ F 4
12AD3SOFTWAREA E:3 , RSQ E:4 , G E:5 , A F:3 , U F:6 , HOH F:104 , HOH F:105 , HOH F:106 , HOH F:108 , HOH F:109 , HOH F:114 , HOH F:126 , HOH F:130 , HOH F:134 , HOH F:135 , HOH F:142binding site for Di-nucleotide RSQ F 4 and G F 5

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

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(-) PROSITE Motifs  (0, 0)

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(-) 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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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:RNA  Length:8
                                      
                   5hnj A 1 GUAxGUAC 8
                               |    
                               |    
                               4-RSQ


Chain B from PDB  Type:RNA  Length:8
                                      
                   5hnj B 1 GUAxGUAC 8
                               |    
                               4-RSQ


Chain C from PDB  Type:RNA  Length:8
                                      
                   5hnj C 1 GUAxGUAC 8
                               |    
                               4-RSQ


Chain D from PDB  Type:RNA  Length:8
                                      
                   5hnj D 1 GUAxGUAC 8
                               |    
                               4-RSQ


Chain E from PDB  Type:RNA  Length:8
                                      
                   5hnj E 1 GUAxGUAC 8
                               |    
                               4-RSQ


Chain F from PDB  Type:RNA  Length:8
                                      
                   5hnj F 1 GUAxGUAC 8
                               |    
                               4-RSQ
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 Classification and Annotation

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5hnq