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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 :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Base Sequence, Binding Sites, Catalysis, Cloning, Molecular, Computer Graphics, Escherichia Coli, Hepatitis Delta Virus, Models, Molecular Sequence Data, Nucleic Acid Conformation, Rna, Catalytic, Viral, Rna-Binding Proteins, Ribonucleoprotein, U1 Small Nuclear, Rna Binding Protein/Rna, 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 - HDV RIBOZYME SELF-CLEAVED
    Chains: B
    Engineered: YES
    Other Details: IN VITRO TRANSCRIPTION
    Synthetic: YES
 
Molecule 2 - U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: T7 EXPRESSION PLASMID (A1-98 Y31H, Q36R)
    Expression System Strain: B834
    Expression System Taxid: 562
    Fragment: RNA BINDING DOMAIN, UNP RESIDUES 101-244
    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  (2, 20)

Asymmetric/Biological Unit (2, 20)
No.NameCountTypeFull Name
1MG16Ligand/IonMAGNESIUM ION
2MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREG B:169 , G B:170BINDING SITE FOR RESIDUE MG B 402
02AC2SOFTWAREC B:152 , A B:153 , HOH B:501BINDING SITE FOR RESIDUE MG B 403
03AC3SOFTWAREG B:138 , HOH B:509BINDING SITE FOR RESIDUE MG B 404
04AC4SOFTWAREG B:117 , C B:118BINDING SITE FOR RESIDUE MG B 406
05AC5SOFTWAREC B:119BINDING SITE FOR RESIDUE MG B 407
06AC6SOFTWAREG B:110BINDING SITE FOR RESIDUE MG B 408
07AC7SOFTWAREG B:135 , C B:136BINDING SITE FOR RESIDUE MG B 409
08AC8SOFTWAREU B:123 , C B:124BINDING SITE FOR RESIDUE MG B 410
09AC9SOFTWAREC B:107BINDING SITE FOR RESIDUE MG B 411
10BC1SOFTWAREC B:107 , A B:108BINDING SITE FOR RESIDUE MG B 412
11BC2SOFTWAREA B:116BINDING SITE FOR RESIDUE MG B 413
12BC3SOFTWARELYS A:23 , LYS A:27BINDING SITE FOR RESIDUE MG A 101
13BC4SOFTWARESER A:48 , LEU A:49 , LYS A:50 , MSE A:51BINDING SITE FOR RESIDUE MG A 102
14BC5SOFTWAREASP A:24BINDING SITE FOR RESIDUE MG A 103

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PR6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4PR6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PR6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PR6)

(-) Exons   (0, 0)

(no "Exon" information available for 4PR6)

(-) 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
                 4pr6 A   4 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKmRGQAFVIFKEVSSATNALRSmQGFPFYDKPmRIQYAKTDSDIIAKmA  98
                                    13        23        33        43       |53        63        73        83        93   | 
                                                                          51-MSE               72-MSE    82-MSE         97-MSE


Chain B from PDB  Type:RNA  Length:72
                                                                                                        
                 4pr6 B 101 GGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACACCAUUGCACUCCGGUGGCGAAUGGGAC 172
                                   110       120       130       140       150       160       170
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  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 1CX0: 1,1)

(no "SCOP Domain" information available for 4PR6, only for superseded entry 1CX0 replaced by 4PR6)

(-) CATH Domains  (0, 0 ; only for superseded entry 1CX0: 1,1)

(no "CATH Domain" information available for 4PR6, only for superseded entry 1CX0 replaced by 4PR6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PR6)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  4pr6
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  SNRPA_HUMAN | P09012
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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 4prf 4w90 4w92 4yb1 5ddo 5ddp 5ddq 5ddr 5fj4

(-) Related Entries Specified in the PDB File

4prf