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(-) Description

Title :  SOLUTION STRUCTURE OF PHD DOMAIN IN PHD FINGER FAMILY PROTEIN
 
Authors :  F. He, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  24 May 04  (Deposition) - 24 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Nmr, Structural Genomics, Phd Domain, Riken Structural Genomics/Proteomics Initiative, Rsgi, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. He, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama
Solution Structure Of Phd Domain In Phd Finger Family Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHD FINGER FAMILY PROTEIN
    Chains: A
    Engineered: YES
    Expression System Plasmid: L030422-A06
    Expression System Vector Type: PLASMID
    Fragment: PHD DOMAIN
    Gene: RAFL09-15-N01
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Other Details: CELL FREE PROTEIN SYNTHESIS

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

NMR Structure (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:19 , CYS A:21 , HIS A:42 , CYS A:45BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWARECYS A:34 , CYS A:37 , CYS A:60 , CYS A:63BINDING SITE FOR RESIDUE ZN A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WEE)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WEE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WEE)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_PHD_1PS01359 Zinc finger PHD-type signature.Y1342_ARATH606-650  1A:19-63

(-) Exons   (0, 0)

(no "Exon" information available for 1WEE)

(-) 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    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:72
 aligned with Y1342_ARATH | Q9C810 from UniProtKB/Swiss-Prot  Length:697

    Alignment length:127
                                   570       580       590       600       610       620       630       640       650       660       670       680       
          Y1342_ARATH   561 GSIDDSITLKFLVGTNGVIRIKGRCSKHGLLRYRMERGVDNWKVDCKCGTKDDDGERMLACDGCGVWHHTRCIGINNADALPSKFLCFRCIELYSKKPKQSKKERGSSQVPKAGFVCRGESAAMGSG 687
               SCOP domains d1w          eea_                  A: PHD finger protein At1g33420                                                              SCOP domains
               CATH domains 1we          eA00                  A:1-72 Zinc/RING finger domain, C3HC4 (zinc finger)                                          CATH domains
               Pfam domains --------------------------------------------PHD-1weeA01 A:18-66                              ---------------------------------- Pfam domains
         Sec.struct. author ...----------....-----------------.......................eee.....eeeehhhh..............hhhhhh.-----------...-----------------.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------ZF_PHD_1  PDB: A:19-63 UniProt: 606-650      ------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wee A   1 GSS----------GSSG-----------------MERGVDNWKVDCKCGTKDDDGERMLACDGCGVWHHTRCIGINNADALPSKFLCFRCIELS-----------GPS-----------------SG  72
                              |      -   |  |  -         -    |   13        23        33        43        53        63   |     -     | | -         -     | 
                              3          4  7                 8                                                         67          68 |                71 
                                                                                                                                      70
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 Classification and Annotation

(-) SCOP Domains  (1, 1)

NMR Structure
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: zf-FYVE-PHD (57)

(-) Gene Ontology  (5, 5)

NMR Structure(hide GO term definitions)
Chain A   (Y1342_ARATH | Q9C810)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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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