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(-) Description

Title :  STRUCTURAL CHARACTERIZATION OF INTERACTIONS BETWEEN THE DOUBLE-STRANDED RNA-BINDING ZINC FINGER PROTEIN JAZ AND DSRNA
 
Authors :  P. Wright, J. Dyson, R. Burge, M. Martinez-Yamout
Date :  10 Feb 14  (Deposition) - 19 Mar 14  (Release) - 27 Apr 16  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C
NMR Structure *:  A,B,C  (1x)
Keywords :  Zinc Finger, Dsrna-Binding, Rna Binding Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. G. Burge, M. A. Martinez-Yamout, H. J. Dyson, P. E. Wright
Structural Characterization Of Interactions Between The Double-Stranded Rna-Binding Zinc Finger Protein Jaz And Nucleic Acids.
Biochemistry V. 53 1495 2014
PubMed-ID: 24521053  |  Reference-DOI: 10.1021/BI401675H

(-) Compounds

Molecule 1 - ZINC FINGER PROTEIN 346
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 181-224
    Gene: ZNF346, JAZ
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - RNA (5'- R(*GP*CP*CP*GP*UP*GP*GP*UP*CP*UP*GP*GP*UP*GP*GP*CP*CP*GP*G)-3')
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - RNA (5'- R(P*CP*CP*GP*GP*CP*CP*AP*CP*CP*AP*GP*AP*CP*CP*AP*CP*GP*GP*C)-3')
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
NMR Structure : ABC
NMR Structure * (1x): ABC

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:187 , CYS A:190 , HIS A:203 , HIS A:209BINDING SITE FOR RESIDUE ZN A 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2MKN)

(-) Exons   (0, 0)

(no "Exon" information available for 2MKN)

(-) 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
(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:44
 aligned with ZN346_HUMAN | Q9UL40 from UniProtKB/Swiss-Prot  Length:294

    Alignment length:44
                                   190       200       210       220    
          ZN346_HUMAN   181 IDPDKFCSLCHATFNDPVMAQQHYVGKKHRKQETKLKLMARYGR 224
               SCOP domains -------------------------------------------- SCOP domains
               CATH domains -------------------------------------------- CATH domains
               Pfam domains -------------------------------------------- Pfam domains
         Sec.struct. author ....ee......ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------- PROSITE
                 Transcript -------------------------------------------- Transcript
                 2mkn A 181 IDPDKFCSLCHATFNDPVMAQQHYVGKKHRKQETKLKLMARYGR 224
                                   190       200       210       220    


Chain B from PDB  Type:RNA  Length:19
                                                   
                 2mkn B   1 GCCGUGGUCUGGUGGCCGG  19
                                    10         


Chain C from PDB  Type:RNA  Length:19
                                                   
                 2mkn C  20 CCGGCCACCAGACCACGGC  38
                                    29
   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 2MKN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2MKN)

(-) Gene Ontology  (13, 13)

NMR Structure(hide GO term definitions)
Chain A   (ZN346_HUMAN | Q9UL40)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003725    double-stranded RNA binding    Interacting selectively and non-covalently with double-stranded RNA.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0002039    p53 binding    Interacting selectively and non-covalently with one of the p53 family of proteins.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0072332    intrinsic apoptotic signaling pathway by p53 class mediator    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, and ends when the execution phase of apoptosis is triggered.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ZN346_HUMAN | Q9UL40: 2mkd

(-) Related Entries Specified in the PDB File

2mkd HADDOCK STARTING STRUCTURE RELATED ID: 17679 RELATED DB: BMRB