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(-) Description

Title :  COOPERATIVITY AND DOWNSTREAM BINDING IN RNA REPLICATION
 
Authors :  W. Zhang, A. C. Fahrenbach, C. P. Tam, J. W. Szostak
Date :  30 Aug 15  (Deposition) - 07 Dec 16  (Release) - 18 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Rna, Monomer, Cooperativity (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. Zhang, C. P. Tam, J. Wang, J. W. Szostak
Unusual Base-Pairing Interactions In Monomer-Template Complexes.
Acs Cent Sci V. 2 916 2016
PubMed-ID: 28058281  |  Reference-DOI: 10.1021/ACSCENTSCI.6B00278

(-) Compounds

Molecule 1 - RNA (5'-R(*(LCC)P*(LCC)P*(LCA)P*(LCG) P*AP*CP*UP*UP*AP*AP*GP*UP*CP*U)-3')
    ChainsA, B, C, D
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    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  (5, 39)

Asymmetric Unit (5, 39)
No.NameCountTypeFull Name
15GP8Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
2LCA4Mod. Nucleotide[(1R,3R,4R,7S)-7-HYDROXY-3-(ADENIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGENPHOSPHATE
3LCC8Mod. Nucleotide[(1R,3R,4R,7S)-7-HYDROXY-3-(5-METHYLCYTOSIN-1-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGENPHOSPHATE
4LCG4Mod. Nucleotide[(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGENPHOSPHATE
5MG15Ligand/IonMAGNESIUM ION
Biological Unit 1 (4, 12)
No.NameCountTypeFull Name
15GP4Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
2LCA2Mod. Nucleotide[(1R,3R,4R,7S)-7-HYDROXY-3-(ADENIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGENPHOSPHATE
3LCC4Mod. Nucleotide[(1R,3R,4R,7S)-7-HYDROXY-3-(5-METHYLCYTOSIN-1-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGENPHOSPHATE
4LCG2Mod. Nucleotide[(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGENPHOSPHATE
5MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (4, 12)
No.NameCountTypeFull Name
15GP4Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
2LCA2Mod. Nucleotide[(1R,3R,4R,7S)-7-HYDROXY-3-(ADENIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGENPHOSPHATE
3LCC4Mod. Nucleotide[(1R,3R,4R,7S)-7-HYDROXY-3-(5-METHYLCYTOSIN-1-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGENPHOSPHATE
4LCG2Mod. Nucleotide[(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGENPHOSPHATE
5MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:206 , HOH A:232 , HOH A:244 , HOH B:240 , HOH B:249 , HOH B:267binding site for residue MG A 101
02AC2SOFTWAREHOH A:230 , HOH A:245 , HOH A:263 , HOH B:201 , HOH B:220 , HOH B:271binding site for residue MG A 102
03AC3SOFTWAREHOH A:212 , HOH A:239 , HOH A:241 , HOH A:262 , HOH A:265 , HOH A:266binding site for residue MG A 103
04AC4SOFTWARE5GP A:105 , HOH A:203 , HOH A:220 , HOH A:236 , U B:14 , MG B:104binding site for residue 5GP A 104
05AC5SOFTWARE5GP A:104 , HOH A:203 , U B:14 , HOH B:221binding site for residue 5GP A 105
06AC6SOFTWAREHOH A:247 , HOH A:257 , HOH A:259 , HOH B:208 , HOH B:237 , HOH B:244binding site for residue MG B 101
07AC7SOFTWAREG B:11 , HOH B:251binding site for residue MG B 102
08AC8SOFTWAREHOH B:210 , HOH B:227 , HOH B:260 , HOH B:268 , HOH B:272 , HOH B:273binding site for residue MG B 103
09AC9SOFTWARE5GP A:104binding site for residue MG B 104
10AD1SOFTWAREU A:14 , 5GP B:106binding site for residue 5GP B 105
11AD2SOFTWAREU A:14 , HOH A:218 , 5GP B:105binding site for residue 5GP B 106
12AD3SOFTWAREHOH C:206 , HOH C:225 , HOH C:237 , HOH D:248 , HOH D:254 , HOH D:268binding site for residue MG C 101
13AD4SOFTWAREHOH C:233 , HOH C:249 , HOH C:264 , HOH D:201 , HOH D:224 , HOH D:273binding site for residue MG C 102
14AD5SOFTWAREHOH C:224 , HOH C:230 , HOH C:248 , HOH C:262 , HOH C:266 , HOH C:267binding site for residue MG C 103
15AD6SOFTWAREHOH C:220 , HOH C:265 , HOH C:268 , HOH D:210 , HOH D:227 , HOH D:274binding site for residue MG C 104
16AD7SOFTWARE5GP C:106 , HOH C:203 , HOH C:227 , U D:14 , MG D:104 , HOH D:232binding site for residue 5GP C 105
17AD8SOFTWARE5GP C:105 , HOH C:203 , U D:14 , HOH D:215binding site for residue 5GP C 106
18AD9SOFTWAREHOH C:246 , HOH C:258 , HOH C:260 , HOH D:220 , HOH D:239 , HOH D:250binding site for residue MG D 101
19AE1SOFTWAREG D:11 , HOH D:258binding site for residue MG D 102
20AE2SOFTWAREHOH D:211 , HOH D:231 , HOH D:264 , HOH D:270 , HOH D:275 , HOH D:276binding site for residue MG D 103
21AE3SOFTWARE5GP C:105binding site for residue MG D 104
22AE4SOFTWAREU C:14 , 5GP D:106 , HOH D:210 , HOH D:227binding site for residue 5GP D 105
23AE5SOFTWAREU C:14 , HOH C:211 , 5GP D:105binding site for residue 5GP D 106

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DHC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DHC)

(-) Exons   (0, 0)

(no "Exon" information available for 5DHC)

(-) 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
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Chain A from PDB  Type:RNA  Length:14
                                             
                  5dhc A  1 xxxxACUUAAGUCU 14
                            ||||    10    
                            ||||          
                            1-LCC         
                             2-LCC        
                              3-LCA       
                               4-LCG      

Chain B from PDB  Type:RNA  Length:14
                                             
                  5dhc B  1 xxxxACUUAAGUCU 14
                            ||||    10    
                            1-LCC         
                             2-LCC        
                              3-LCA       
                               4-LCG      

Chain C from PDB  Type:RNA  Length:14
                                             
                  5dhc C  1 xxxxACUUAAGUCU 14
                            ||||    10    
                            1-LCC         
                             2-LCC        
                              3-LCA       
                               4-LCG      

Chain D from PDB  Type:RNA  Length:14
                                             
                  5dhc D  1 xxxxACUUAAGUCU 14
                            ||||    10    
                            1-LCC         
                             2-LCC        
                              3-LCA       
                               4-LCG      

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 5DHC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DHC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DHC)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5DHC)

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 Related Entries

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(-) Related Entries Specified in the PDB File

5dhb 5hbw 5hbx 5hby 5krg 5l00