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(-) Description

Title :  SOLUTION STRUCTURE OF THE 6TH C2H2 TYPE ZINC FINGER DOMAIN OF ZINC FINGER PROTEIN 484
 
Authors :  M. Imai, S. Suzuki, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  30 Mar 07  (Deposition) - 02 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  C2H2, Zinc Finger Domain, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Imai, S. Suzuki, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama
Solution Structure Of The 6Th C2H2 Type Zinc Finger Domain Of Zinc Finger Protein 484
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ZINC FINGER PROTEIN 484
    ChainsA
    EngineeredYES
    Expression System PlasmidP070115-39
    Expression System Vector TypePLASMID
    FragmentZINC FINGER DOMAIN
    GeneZNF484
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (0, 0)

(no "Site" information available for 2EQW)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_FINGER_C2H2_1PS00028 Zinc finger C2H2 type domain signature.ZN484_HUMAN386-406
414-434
442-462
470-490
498-518
526-546
554-574
582-602
610-630
638-658
666-686
694-714
722-742
750-770
778-798
  2-
A:414-434
A:439-441
-
-
-
-
-
-
-
-
-
-
-
-

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003754951bENSE00001423546chr9:95640290-95640172119ZN484_HUMAN-00--
1.2ENST000003754952ENSE00002185623chr9:95637341-9563729745ZN484_HUMAN1-550--
1.4ENST000003754954ENSE00001785280chr9:95618600-95618474127ZN484_HUMAN6-48430--
1.5ENST000003754955ENSE00000869903chr9:95618185-9561809393ZN484_HUMAN48-79320--
1.6bENST000003754956bENSE00001521895chr9:95610833-956083512483ZN484_HUMAN79-8527741A:402-443 (gaps)169

(-) 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:42
 aligned with ZN484_HUMAN | Q5JVG2 from UniProtKB/Swiss-Prot  Length:852

    Alignment length:169
                                   305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455         
          ZN484_HUMAN   296 GSQRVYAGICTEYEKDFSLKSNRQKTPYEGNYYKCSDYGRAFIQKSDLFRCQRIHSGEKPYEYSECEKNLPQNSNLNIHKKIHTGGKHFECTECGKAFTRKSTLSMHQKIHTGEKPYVCTECGKAFIRKSHFITHERIHTGEKPYECSDCGKSFIKKSQLHVHQRIHTG 464
               SCOP domains ---------------------------------------------------------------------------------------------------------------d2eqwa1 A:407-434           ------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..-----------------------------------------------------...-----------------------------------------------------.....ee......ee...hhhhhhhhhhh..-------....--------------.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1   -- PROSITE
               Transcript 1 Exon 1.6b  PDB: A:402-443 (gaps) UniProt: 79-852 [INCOMPLETE]                                                                                                             Transcript 1
                 2eqw A 402 GS-----------------------------------------------------SGS-----------------------------------------------------SGEKPYVCTECGKAFIRKSHFITHERIHTGE-------SGPS--------------SG 443
                             |       -         -         -         -         -     | | -         -         -         -         -         - |     415       425       435 |     438  |      -       | 
                             |                                                   404 |                                                   407                           437     438  |            442 
                           403                                                     406                                                                                            441                

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 1)

NMR Structure

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

NMR Structure(hide GO term definitions)
Chain A   (ZN484_HUMAN | Q5JVG2)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    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
        ZN484_HUMAN | Q5JVG22emf 2emg 2emh 2emi 2eov 2ep1 2ep2 2ep3 2ytj 2yto 2ytp 2yts

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