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(-) Description

Title :  A SECOND LOOK AT THE HDV RIBOZYME STRUCTURE AND DYNAMICS.
 
Authors :  G. J. Kapral, S. Jain, J. Noeske, J. A. Doudna, D. C. Richardson, J. S. Ric
Date :  05 Mar 14  (Deposition) - 29 Oct 14  (Release) - 26 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hdv, Ribozyme, Rna, U1A, Precursor, Translation-Rna Complex, Rna Binding Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. J. Kapral, S. Jain, J. Noeske, J. A. Doudna, D. C. Richardson, J. S. Richardson
New Tools Provide A Second Look At Hdv Ribozyme Structure, Dynamics And Cleavage.
Nucleic Acids Res. V. 42 12833 2014
PubMed-ID: 25326328  |  Reference-DOI: 10.1093/NAR/GKU992

(-) Compounds

Molecule 1 - HEPATITIS DELTA VIRUS RIBOZYME
    Chains: B
    Engineered: YES
    Other Details: RNA OCCURS FROM HAPATITIS DELTA VIRUS PATHOGEN, IN VITRO TRANSCRIPTION WITH PUC19
    Synthetic: YES
 
Molecule 2 - U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: U1A_RBD, UNP RESIDUES 98-173
    Gene: SNRPA
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: U1 SNRNP A, U1-A, U1A

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1SR2Ligand/IonSTRONTIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREU B:120 , U B:123 , U B:163BINDING SITE FOR RESIDUE SR B 201
2AC2SOFTWAREC B:141BINDING SITE FOR RESIDUE SR B 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PRF)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4PRF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PRF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PRF)

(-) Exons   (0, 0)

(no "Exon" information available for 4PRF)

(-) 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
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:95
                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee......hhhhhhhhhhhhhhhhh.eeeeee.........eeeee.hhhhhhhhhhhhh..ee..ee.eeee....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 4prf A   4 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMK  98
                                    13        23        33        43        53        63        73        83        93     


Chain B from PDB  Type:RNA  Length:74
                                                                                                          
                 4prf B  99 AUGGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACACCAUUGCACUCCGGUGGUGAAUGGGAC 172
                                   108       118       128       138       148       158       168
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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 ; only for superseded entry 1VC7: 1,1)

(no "SCOP Domain" information available for 4PRF, only for superseded entry 1VC7 replaced by 4PRF)

(-) CATH Domains  (0, 0 ; only for superseded entry 1VC7: 1,1)

(no "CATH Domain" information available for 4PRF, only for superseded entry 1VC7 replaced by 4PRF)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PRF)

(-) Gene Ontology  (16, 16)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SNRPA_HUMAN | P09012: 1aud 1drz 1dz5 1fht 1m5k 1m5o 1m5p 1m5v 1nu4 1oia 1sj3 1sj4 1sjf 1u6b 1urn 1vbx 1vby 1vbz 1vc0 1vc5 1vc6 1zzn 2a3j 2nz4 2oih 2oj3 2u1a 3bo2 3bo3 3bo4 3cul 3cun 3egz 3g8s 3g8t 3g96 3g9c 3hhn 3iin 3irw 3iwn 3k0j 3l3c 3mum 3mur 3mut 3muv 3mxh 3p49 3pgw 3r1h 3r1l 3ucu 3ucz 3ud3 3ud4 3utr 4c4w 4pr6 4w90 4w92 4yb1 5ddo 5ddp 5ddq 5ddr 5fj4

(-) Related Entries Specified in the PDB File

4pr6 THE POST-CLEAVED HDV RIBOZYME REREFINED WITH ERRASER AND PHENIX