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(-) Description

Title :  SOLUTION STRUCTURE OF THE N-TERMINAL C2H2 TYPE ZINC-BINDING DOMAIN OF THE ZINC FINGER PROTEIN 64, ISOFORMS 1 AND 2
 
Authors :  M. Yoneyama, N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  21 Apr 06  (Deposition) - 21 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Zinc Finger Protein 338, Znf338, Nuclear Protein, Dna- Binding, Transcription, C2H2-Type Zinc Finger, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Yoneyama, N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The N-Terminal C2H2 Type Zinc-Binding Domain Of The Zinc Finger Protein 64, Isoforms 1 And 2
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ZINC FINGER PROTEIN 64, ISOFORMS 1 AND 2
    ChainsA
    EngineeredYES
    Expression SystemCELL FREE SYNTHESIS
    Expression System PlasmidP050815-12
    Expression System Vector TypePLASMID
    FragmentC2H2-TYPE ZINC-BINDING DOMAIN
    GeneZFP64
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymZINC FINGER PROTEIN 338

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

NMR Structure (1, 3)
No.NameCountTypeFull Name
1ZN3Ligand/IonZINC ION

(-) Sites  (3, 3)

NMR Structure (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:11 , VAL A:13 , CYS A:14 , HIS A:27 , HIS A:31BINDING SITE FOR RESIDUE ZN A 191
2AC2SOFTWARECYS A:39 , CYS A:42 , HIS A:55 , HIS A:59BINDING SITE FOR RESIDUE ZN A 241
3AC3SOFTWARECYS A:67 , CYS A:70 , HIS A:83 , HIS A:87BINDING SITE FOR RESIDUE ZN A 291

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_FINGER_C2H2_1PS00028 Zinc finger C2H2 type domain signature.ZF64A_HUMAN177-197
261-281
289-310
345-365
427-447
  1A:11-31
-
-
-
-

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000002169232aENSE00001882484chr20:50808525-50808130396ZF64A_HUMAN1-16160--
1.3aENST000002169233aENSE00001688221chr20:50803610-50803371240ZF64A_HUMAN16-96811A:1-66
1.5ENST000002169235ENSE00001660242chr20:50782564-50782403162ZF64A_HUMAN96-150550--
1.6ENST000002169236ENSE00001689419chr20:50781296-5078123463ZF64A_HUMAN150-171220--
1.7bENST000002169237bENSE00000662759chr20:50776913-50776662252ZF64A_HUMAN171-255851A:7-89 (gaps)85
1.15aENST0000021692315aENSE00001455405chr20:50769967-507678172151ZF64A_HUMAN255-6814271A:89-96 (gaps)58

(-) 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:96
 aligned with ZF64A_HUMAN | Q9NPA5 from UniProtKB/Swiss-Prot  Length:681

    Alignment length:255
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307     
          ZF64A_HUMAN    58 GTSAAAPSTVQFVSEETVPATQTQTTTRTITSETQTITVSAPEFVFEHGYQTYLPTESNENQTATVISLPAKSRTKKPTTPPAQKRLNCCYPGCQFKTAYGMKDMERHLKIHTGDKPHKCEVCGKCFSRKDKLKTHMRCHTGVKPYKCKTCDYAAADSSSLNKHLRIHSDERPFKCQICPYASRNSSQLTVHLRSHTGDAPFQCWLCSAKFKISSDLKRHMRVHSGEKPFKCEFCNVRCTMKGNLKSHIRIKHSG 312
               SCOP domains --------------------------------------------------------------------------------------------------------------------d2dmda2 A:8-33            d2dmda1 A:34-61             d2dmda3 A:62-90              -------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......-----------------------------------------------------------------------------------------------------------.--............hhhhhhhhhhhh.....ee......ee.hhhhhhhhhhhh.....ee......ee.hhhhhhhhhh.....-------------------------....-------------------------.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------ZINC_FINGER_C2H2_1   ---------------------------------------------------------------ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1    -- PROSITE
           Transcript 1 (1) Exon 1.3a  PDB: A:1-6 UniProt: 16-96   -----------------------------------------------------Exon 1.6  PDB: -      -----------------------------------------------------------------------------------Exon 1.15a  PDB: A:89-96 (gaps) UniProt: 255-681           Transcript 1 (1)
           Transcript 1 (2) --------------------------------------Exon 1.5  PDB: - UniProt: 96-150                       --------------------Exon 1.7b  PDB: A:7-89 (gaps) UniProt: 171-255                                       --------------------------------------------------------- Transcript 1 (2)
                 2dmd A   1 GSSGSS-----------------------------------------------------------------------------------------------------------G--PHKCEVCGKCFSRKDKLKTHMRCHTGVKPYKCKTCDYAAADSSSLNKHLRIHSDERPFKCQICPYASRNSSQLTVHLRSHTGD-------------------------SGPS-------------------------SG  96
                                 |   -         -         -         -         -         -         -         -         -         -         -   |  | 11        21        31        41        51        61        71        81        |-         -         -    |  | -         -         -   | 
                                 6                                                                                                           7  8                                                                                90                        91 94                        95 

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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, 3)

NMR Structure

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

NMR Structure(hide GO term definitions)
Chain A   (ZF64A_HUMAN | Q9NPA5)
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: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).
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: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
        ZF64A_HUMAN | Q9NPA51x5w

(-) Related Entries Specified in the PDB File

1x5w THE DIFFERENT FRAGMENT FROM THE SAME PROTEIN RELATED ID: HSS001003730.2 RELATED DB: TARGETDB