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(-) Description

Title :  SOLUTION STRUCTURE OF THE C2H2 TYPE ZINC FINGER (REGION 426-458) OF HUMAN ZINC FINGER PROTEIN 473
 
Authors :  T. Tomizawa, N. Tochio, H. Abe, K. Saito, H. Li, M. Sato, S. Koshiba, N. Kobayashi, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  05 Apr 07  (Deposition) - 09 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Zf-C2H2, Nmr, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Tochio, T. Tomizawa, H. Abe, K. Saito, H. Li, M. Sato, S. Koshiba, N. Kobayashi, T. Kigawa, S. Yokoyama
Solution Structure Of The C2H2 Type Zinc Finger (Region 426-458) Of Human Zinc Finger Protein 473
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ZINC FINGER PROTEIN 473
    Chains: A
    Engineered: YES
    Expression System Plasmid: P070115-57
    Expression System Vector Type: PLASMID
    Fragment: ZF-C2H2
    Gene: ZNF473
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CELL-FREE PROTEIN SYNTHESIS
    Synonym: ZINC FINGER PROTEIN 100 HOMOLOG, ZFP-100

 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  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:15 , CYS A:18 , HIS A:31 , HIS A:35BINDING SITE FOR RESIDUE ZN A 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_FINGER_C2H2_1PS00028 Zinc finger C2H2 type domain signature.ZN473_HUMAN211-231
322-342
349-369
377-397
433-453
461-481
489-509
517-537
564-584
593-613
648-668
676-696
704-724
732-752
760-780
788-808
816-836
844-864		  2-
-
-
-
A:15-35
A:41-44
-
-
-
-
-
-
-
-
-
-
-
-

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003918211ENSE00001600755chr19:50529212-50529379168ZN473_HUMAN-00--
1.2bENST000003918212bENSE00001509820chr19:50534271-5053434878ZN473_HUMAN1-330--
1.3ENST000003918213ENSE00001382389chr19:50542418-50542544127ZN473_HUMAN4-46430--
1.4ENST000003918214ENSE00000954737chr19:50544987-5054507690ZN473_HUMAN46-76310--
1.5aENST000003918215aENSE00001307401chr19:50547927-505520294103ZN473_HUMAN76-8717961A:1-46 (gaps)168

(-) 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:46
 aligned with ZN473_HUMAN | Q8WTR7 from UniProtKB/Swiss-Prot  Length:871

    Alignment length:168
                                   390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540        
          ZN473_HUMAN   381 GKIFRHSSLLIEHQALHAGEEPYKCNERGKSFRHNSTLKIHQRVHSGEKPYKCSECGKAFHRHTHLNEHRRIHTGYRPHKCQECVRSFSRPSHLMRHQAIHTAEKPYSCAECKETFSDNNRLVQHQKMHTVKTPYECQECGERFICGSTLKCHESVHAREKQGFFVSG 548
               SCOP domains ---------------------------------------------d2ytda1 A:8-35              ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ----------------------------------------------------------------zf-H2C2_2-2ytd------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------zf-H2C2_2-2ytd------------------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author .-----..--------------------.------..-------......ee......ee.hhhhhhhhhhhhh....----------....--------------------------------------------------------------------------.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ZINC_FINGER_C2H2_-----------------------------------ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1   -------ZINC_FINGER_C2H2_1   ----------- PROSITE
               Transcript 1 Exon 1.5a  PDB: A:1-46 (gaps) UniProt: 76-871 [INCOMPLETE]                                                                                                               Transcript 1
                 2ytd A   1 G-----SS--------------------G------SS-------GSGEKPYKCSECGKAFHRHTHLNEHRRIHTGYRP----------SGPS--------------------------------------------------------------------------SG  46
                            |     || -         -        |-     ||  -    |   12        22        32       | -        42 |       -         -         -         -         -         -         -      | 
                            |     2|                    4      5|       7                               40         41 44                                                                         45 
                            1      3                            6
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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
(-)
Class: Small proteins (3458)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

NMR Structure
(-)
Clan: C2H2-zf (71)

(-) Gene Ontology  (12, 12)

NMR Structure(hide GO term definitions)
Chain A   (ZN473_HUMAN | Q8WTR7)
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:0008334    histone mRNA metabolic process    The chemical reactions and pathways involving an mRNA encoding a histone.
    GO:0006398    mRNA 3'-end processing by stem-loop binding and cleavage    Any mRNA 3'-end processing that involves the binding to and cleavage of a stem-loop structure. For example, histone mRNAs contain a highly conserved stem-loop sequence at the 3' end of the mRNA with a 6 base pairs (bp) stem and a 4-nt loop. The mRNA is cleaved between these two elements, after the fourth or fifth nucleotide, which is typically an adenosine.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006369    termination of RNA polymerase II transcription    The process in which the synthesis of an RNA molecule by RNA polymerase II using a DNA template is completed.
cellular component
    GO:0015030    Cajal body    A class of nuclear body, first seen after silver staining by Ramon y Cajal in 1903, enriched in small nuclear ribonucleoproteins, and certain general RNA polymerase II transcription factors; ultrastructurally, they appear as a tangle of coiled, electron-dense threads roughly 0.5 micrometers in diameter; involved in aspects of snRNP biogenesis; the protein coilin serves as a marker for Cajal bodies. Some argue that Cajal bodies are the sites for preassembly of transcriptosomes, unitary particles involved in transcription and processing of RNA.
    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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ZN473_HUMAN | Q8WTR7: 2emb 2emc 2eme 2eou 2eox 2eoy 2eoz 2yrh 2yrj 2ysv 2yte 2ytt 2yu5

(-) Related Entries Specified in the PDB File

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