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(-) Description

Title :  SOLUTION STRUCTURE OF PHD DOMAIN IN PROTEIN NP_082203
 
Authors :  F. He, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  25 May 04  (Deposition) - 25 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, Gene Regulation (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 Protein Np_082203
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIKEN CDNA 1110020M19
    Chains: A
    Engineered: YES
    Expression System Plasmid: P030722-17
    Expression System Vector Type: PLASMID
    Fragment: PHD DOMAIN
    Gene: RIKEN CDNA 2810027J24
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: CELL FREE PROTEIN SYNTHESIS
    Synonym: PROTEIN NP_082203

 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:22 , HIS A:44 , CYS A:47BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWARECYS A:36 , CYS A:39 , CYS A:66 , CYS A:69BINDING SITE FOR RESIDUE ZN A 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_PHD_2PS50016 Zinc finger PHD-type profile.INT12_MOUSE158-214  1A:16-72
2ZF_PHD_1PS01359 Zinc finger PHD-type signature.INT12_MOUSE161-211  1A:19-69

(-) Exons   (0, 0)

(no "Exon" information available for 1WEV)

(-) 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:88
 aligned with INT12_MOUSE | Q9D168 from UniProtKB/Swiss-Prot  Length:461

    Alignment length:239
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309         
          INT12_MOUSE    80 GSSNGKVLTAEKIKKEAEKRPADKMKDVTEGIDVPKKPRLEKPETRSSPITVQTSKDLSMADLSSFEETSADDFAMEMGLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQMKRMAQKTQKPPQKPAPTVVSVTPTVKDPLVKKPETKLKQETTFLAFKRTEVKPSTVISGNSSSNNVSSSVTSGLTGWAAFAAKTSSAGPSTAKLNSAAQNSSG 318
               SCOP domains d1w e                                         va                     _ A: PHD finger protein 22                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------1wevA01 A:11-74 Zinc/RING finger domain, C3HC4 (zinc finger)    ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains --------------------------------------------------------------------------------PHD-1wevA01 A:18-72                                    -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...-.-----------------------------------------..---------------------.....hhhh.................eee......eee.........hhhhh........hhhhhhh.........-----------------------------------------------------------------------------...-----------... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------------------------------------ZF_PHD_2  PDB: A:16-72 UniProt: 158-214                  -------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------ZF_PHD_1  PDB: A:19-69 UniProt: 161-211            ----------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wev A   1 GSS-G-----------------------------------------SS---------------------GADDFAMEMGLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQMKRMAQKNQK-----------------------------------------------------------------------------SGP-----------SSG  88
                              | |    -         -         -         -      || -         -         7        17        27        37        47        57        67        77    |    -         -         -         -         -         -         -         -  | |    -      |  
                              3 4                                         5|                     7                                                                         82                                                                            83 |          86  
                                                                           6                                                                                                                                                                               85
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  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  (1, 1)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (6, 6)

NMR Structure(hide GO term definitions)
Chain A   (INT12_MOUSE | Q9D168)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0016180    snRNA processing    Any process involved in the conversion of a primary small nuclear RNA (snRNA) transcript into a mature snRNA molecule.
cellular component
    GO:0032039    integrator complex    A protein complex that stably associates with the C-terminus of RNA polymerase II and mediates 3'-end processing of small nuclear RNAs generated by RNA polymerase II.
    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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