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(-) Description

Title :  SOLUTION STRUCTURE OF PHD DOMAIN IN PHD FINGER PROTEIN 7
 
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, Phd Finger Protein 7, 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 Phd Finger Protein 7
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHD FINGER PROTEIN 7
    Chains: A
    Engineered: YES
    Expression System Plasmid: P030408-45
    Expression System Vector Type: PLASMID
    Fragment: PHD DOMAIN
    Gene: RIKEN CDNA 1700010P14
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    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:24 , CYS A:29 , THR A:57 , HIS A:58 , CYS A:61BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWARECYS A:49 , CYS A:52 , CYS A:73 , CYS A:76BINDING SITE FOR RESIDUE ZN A 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WEQ)

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENSMUST000000224591aENSMUSE00000235231chr14:32064404-32063891514PHF7_MOUSE-00--
1.2ENSMUST000000224592ENSMUSE00000235224chr14:32062903-32062794110PHF7_MOUSE1-14140--
1.3ENSMUST000000224593ENSMUSE00000121852chr14:32062233-3206218153PHF7_MOUSE14-32190--
1.4ENSMUST000000224594ENSMUSE00000121845chr14:32061320-3206122992PHF7_MOUSE32-62310--
1.5ENSMUST000000224595ENSMUSE00000121848chr14:32055013-32054912102PHF7_MOUSE63-96340--
1.6ENSMUST000000224596ENSMUSE00000121847chr14:32054169-32054045125PHF7_MOUSE97-138420--
1.7ENSMUST000000224597ENSMUSE00000121850chr14:32053619-32053460160PHF7_MOUSE138-191541A:1-44
1.8ENSMUST000000224598ENSMUSE00000121849chr14:32052923-32052817107PHF7_MOUSE192-227361A:5-73
1.9ENSMUST000000224599ENSMUSE00000121851chr14:32052422-32052306117PHF7_MOUSE227-266401A:8-4235
1.10ENSMUST0000002245910ENSMUSE00000235167chr14:32051668-32051523146PHF7_MOUSE266-307421A:42-8342
1.11bENSMUST0000002245911bENSMUSE00000235163chr14:32051339-32050882458PHF7_MOUSE-00--

(-) 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:85
 aligned with PHF7_MOUSE | Q9DAG9 from UniProtKB/Swiss-Prot  Length:307

    Alignment length:157
                                                                                                                                                                                    307  
                                   162       172       182       192       202       212       222       232       242       252       262       272       282       292       302    |  
           PHF7_MOUSE   153 GSLGEESCVLCCENLSRTSVENIQSPCCSQAIYHRKCIQKYAHTSAKHFFKCPQCNNREEFPQEMLRMGIHIPDRDAAWELEPGAFSELYQRYRHCDAPICLYEQGRDSFEDEGRWRLILCATCGSHGTHRDCSSLRPNSKKWECNECLPASTTS--   -
               SCOP domains d1we                                       qa_                                  A: PHD finger protein 7 (NYD-SP6)                                             SCOP domains
               CATH domains 1weq                                       A00                                  A:1-85 Zinc/RING finger domain, C3HC4 (zinc finger)                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....---------------------------------------...---------------------------------.......................................ee.......ee..hhh...........hhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.7  PDB: A:1-4 UniProt: 138-191  Exon 1.8  PDB: A:5-7 [INCOMPLETE]   --------------------------------------Exon 1.10  PDB: A:42-83 UniProt: 266-307  -- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------Exon 1.9  PDB: A:8-42 UniProt: 227-266  ------------------------------------------- Transcript 1 (2)
                 1weq A   1 GSSG---------------------------------------SSG---------------------------------ELEPGAFSELYQRYRHCDAPICLYEQGRDSFEDEGRWRLILCATCGSHGTHRDCSSLRPNSKKWECNECLPASGPSSG  85
                               |     -         -         -         -   | |   -         -         -         8        18        28        38        48        58        68        78       
                               4                                       5 7                                 8
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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  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1WEQ)

(-) Gene Ontology  (6, 6)

NMR Structure(hide GO term definitions)
Chain A   (PHF7_MOUSE | Q9DAG9)
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:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
cellular component
    GO:0005815    microtubule organizing center    An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
    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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