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(-) Description

Title :  U11-48K CHHC ZN-FINGER PROTEIN DOMAIN
 
Authors :  H. Tidow, A. Andreeva, T. J. Rutherford, A. R. Fersht
Date :  18 Jul 08  (Deposition) - 17 Feb 09  (Release) - 18 Apr 12  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A
NMR Structure *:  A  (1x)
Keywords :  Splicing, Mrna Processing, Alternative Splicing, Transcription, Nucleus, Spliceosome, Polymorphism, Mrna Splicing (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Tidow, A. Andreeva, T. J. Rutherford, A. R. Fersht
Solution Structure Of The U11-48K Chhc Zinc-Finger Domain That Specifically Binds The 5 Splice Site Of U12-Type Introns
Structure V. 17 294 2009
PubMed-ID: 19217400  |  Reference-DOI: 10.1016/J.STR.2008.11.013

(-) Compounds

Molecule 1 - U11/U12 SMALL NUCLEAR RIBONUCLEOPROTEIN 48 KDA PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainC41
    Expression System Taxid562
    Expression System VectorPRSET
    FragmentRESIDUES 53-87
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymU11/U12 SNRNP 48 KDA PROTEIN, U11/U12-48K, U11-48K CHHC ZN-FINGER

 Structural Features

(-) Chains, Units

  1
NMR Structure A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION
NMR Structure * (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:58 , HIS A:64 , MET A:66 , HIS A:74 , CYS A:78BINDING SITE FOR RESIDUE ZN A1088

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VY5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2VY5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VY5)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_CHHC_U11_48KPS51800 Zinc finger CHHC U11-48K-type profile.SNR48_HUMAN55-82  1A:55-82
NMR Structure * (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_CHHC_U11_48KPS51800 Zinc finger CHHC U11-48K-type profile.SNR48_HUMAN55-82  1A:55-82

(-) Exons   (0, 0)

(no "Exon" information available for 2VY5)

(-) Sequences/Alignments

NMR Structure
   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:PROTEIN  Length:37
 aligned with SNR48_HUMAN | Q6IEG0 from UniProtKB/Swiss-Prot  Length:339

    Alignment length:42
                                    55        65        75        85  
           SNR48_HUMAN   46 GEEEAAEDEVVICPYDSNHHMPKSSLAKHMASCRLRKMGYTK 87
               SCOP domains -------d2vy5a1 A:53-87                     SCOP domains
               CATH domains ------------------------------------------ CATH domains
               Pfam domains --------zf-U11-48K-2vy5A01 A:54-80 ------- Pfam domains
         Sec.struct. author ..-----...eee....eeee....hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------ SAPs(SNPs)
                    PROSITE ---------ZF_CHHC_U11_48K  PDB: A:55-8----- PROSITE
                 Transcript ------------------------------------------ Transcript
                  2vy5 A 51 GS-----DEVVICPYDSNHHMPKSSLAKHMASCRLRKMGYTK 87
                             |     |55        65        75        85  
                             |    53                                  
                            52                                        

   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  (1, 1)

NMR Structure

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2VY5)

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (9, 9)

NMR Structure(hide GO term definitions)
Chain A   (SNR48_HUMAN | Q6IEG0)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0008380    RNA splicing    The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0000398    mRNA splicing, via spliceosome    The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
cellular component
    GO:0005689    U12-type spliceosomal complex    Any spliceosomal complex that forms during the splicing of a messenger RNA primary transcript to excise an intron; the series of U12-type spliceosomal complexes is involved in the splicing of the majority of introns that contain atypical AT-AC terminal dinucleotides, as well as other non-canonical introns. The entire splice site signal, not just the terminal dinucleotides, is involved in determining which spliceosome utilizes the site.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005681    spliceosomal complex    Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SNR48_HUMAN | Q6IEG02vy4

(-) Related Entries Specified in the PDB File

2vy4 U11-48K CHHC ZN-FINGER PROTEIN DOMAIN