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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 :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Rna, Cooperativity, Monomer (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*(TLN)P*(LCG)P*UP*AP*CP*A)-3')
    Chains: A, B, C, D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 16)

Asymmetric/Biological Unit (4, 16)
No.NameCountTypeFull Name
15GP4Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
2LCC4Mod. Nucleotide[(1R,3R,4R,7S)-7-HYDROXY-3-(5-METHYLCYTOSIN-1-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGENPHOSPHATE
3LCG4Mod. Nucleotide[(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGENPHOSPHATE
4TLN4Mod. Nucleotide[(1R,3R,4R,7S)-7-HYDROXY-3-(THYMIN-1-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGENPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREA A:7 , HOH A:208 , HOH A:215 , C C:6 , A C:7binding site for residue 5GP A 101
2AC2SOFTWAREA B:7 , HOH B:206 , HOH B:208binding site for residue 5GP B 101
3AC3SOFTWAREA C:7 , HOH C:209binding site for residue 5GP C 101
4AC4SOFTWAREC B:6 , A B:7 , A D:7 , HOH D:209 , HOH D:213binding site for residue 5GP D 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DHB)

(-) Sequences/Alignments

Asymmetric/Biological 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:7
                                     
                   5dhb A 1 xxxUACA 7
                            |||    
                            |||    
                            1-LCC  
                             2-TLN 
                              3-LCG


Chain B from PDB  Type:RNA  Length:7
                                     
                   5dhb B 1 xxxUACA 7
                            |||    
                            |||    
                            1-LCC  
                             2-TLN 
                              3-LCG


Chain C from PDB  Type:RNA  Length:7
                                     
                   5dhb C 1 xxxUACA 7
                            |||    
                            |||    
                            1-LCC  
                             2-TLN 
                              3-LCG


Chain D from PDB  Type:RNA  Length:7
                                     
                   5dhb D 1 xxxUACA 7
                            |||    
                            |||    
                            1-LCC  
                             2-TLN 
                              3-LCG
   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 5DHB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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  5dhb
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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

5dhc 5hbw 5hbx 5hby 5krg 5l00