Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - model 1, sites
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - model 1, sites
NMR Structure - model 1, sites  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF PHD DOMAIN IN INHIBITOR OF GROWTH PROTEIN 3 (ING3)
 
Authors :  F. He, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  14 May 05  (Deposition) - 14 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Nmr, Structural Genomics, Phd Domain, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Cell Adhesion (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 Inhibitor Of Growth Protein 3 (Ing3)
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INHIBITOR OF GROWTH PROTEIN 3
    ChainsA
    EngineeredYES
    Expression System PlasmidP040705-02
    Expression System Vector TypePLASMID
    FragmentPHD DOMAIN
    GeneSCRIB;
CRIB1;
KIAA0147;
LAP4;
SCRB
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL FREE PROTEIN SYNTHESIS
    SynonymP47ING3 PROTEIN, HSPC301, LAP4 PROTEIN, SCRIBBLE HOMOLOG PROTEIN, HSCRIB

 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:9 , CYS A:11 , HIS A:33 , CYS A:36BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWARECYS A:22 , CYS A:27 , CYS A:49 , CYS A:52BINDING SITE FOR RESIDUE ZN A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X4I)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1X4I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X4I)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_PHD_2PS50016 Zinc finger PHD-type profile.ING3_HUMAN360-409  1A:8-55
2ZF_PHD_1PS01359 Zinc finger PHD-type signature.ING3_HUMAN363-406  1A:9-52

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003158701aENSE00001928540chr7:120590803-120590978176ING3_HUMAN1-10100--
1.2bENST000003158702bENSE00000881961chr7:120591218-12059128972ING3_HUMAN10-34250--
1.3ENST000003158703ENSE00000881962chr7:120593358-120593458101ING3_HUMAN34-67340--
1.4aENST000003158704aENSE00000881963chr7:120595613-12059567866ING3_HUMAN68-89220--
1.5ENST000003158705ENSE00001344252chr7:120604796-12060489297ING3_HUMAN90-122330--
1.6ENST000003158706ENSE00001707579chr7:120606680-12060675172ING3_HUMAN122-146250--
1.7bENST000003158707bENSE00001747066chr7:120607583-120607702120ING3_HUMAN146-186410--
1.8ENST000003158708ENSE00001708779chr7:120607988-120608145158ING3_HUMAN186-238530--
1.9ENST000003158709ENSE00001669692chr7:120609065-120609258194ING3_HUMAN239-303650--
1.10ENST0000031587010ENSE00001750048chr7:120610742-120610934193ING3_HUMAN303-367651A:1-13 (gaps)53
1.11ENST0000031587011ENSE00001734073chr7:120613259-12061329739ING3_HUMAN368-380131A:14-2613
1.12cENST0000031587012cENSE00001344212chr7:120614782-1206172702489ING3_HUMAN381-418381A:27-6438

(-) 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:70
 aligned with ING3_HUMAN | Q9NXR8 from UniProtKB/Swiss-Prot  Length:418

    Alignment length:110
                                                                                                                                 418      
                                   324       334       344       354       364       374       384       394       404       414   |     -
           ING3_HUMAN   315 SSSSSSSLSSCSSSSTVVQEISQQTTVVPESDSNSQVDWTYDPNEPRYCICNQVSYGEMVGCDNQDCPIEWFHYGCVGLTEAPKGKWYCPQCTAAMKRRGSRHK------   -
               SCOP domains d1x4ia_                                         A: automated matches                                           SCOP domains
               CATH domains 1x4iA00                                         A:1-70 Zinc/RING finger domain, C3HC4 (zinc finger)            CATH domains
               Pfam domains -----------------------------------------------PHD-1x4iA01 A:8-55                              --------------- Pfam domains
         Sec.struct. author .......----------------------------------------...........ee...........eehhhh...............hhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------------------ZF_PHD_2  PDB: A:8-55 UniProt: 360-409            --------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------ZF_PHD_1  PDB: A:9-52 UniProt: 363-406      ------------------ PROSITE (2)
               Transcript 1 Exon 1.10  PDB: A:1-13 (gaps) UniProt: 303-367       Exon 1.11    Exon 1.12c  PDB: A:27-64              ------ Transcript 1
                 1x4i A   1 GSSGSSG----------------------------------------YCICNQVSYGEMVGCDNQDCPIEWFHYGCVGLTEAPKGKWYCPQCTAAMKRRGSRHKSGPSSG  70
                                  |  -         -         -         -       |10        20        30        40        50        60        70
                                  7                                        8                                                              

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (17, 17)

NMR Structure(hide GO term definitions)
Chain A   (ING3_HUMAN | Q9NXR8)
molecular function
    GO:0004402    histone acetyltransferase activity    Catalysis of the reaction: acetyl-CoA + histone = CoA + acetyl-histone.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0035064    methylated histone binding    Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0043968    histone H2A acetylation    The modification of histone H2A by the addition of an acetyl group.
    GO:0043967    histone H4 acetylation    The modification of histone H4 by the addition of an acetyl group.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0040008    regulation of growth    Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development.
    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:0035267    NuA4 histone acetyltransferase complex    A complex having histone acetylase activity on chromatin, as well as ATPase, DNA helicase and structural DNA binding activities. The complex is thought to be involved in double-strand DNA break repair. Subunits of the human complex include HTATIP/TIP60, TRRAP, RUVBL1, BUVBL2, beta-actin and BAF53/ACTL6A. In yeast, the complex has 13 subunits, including the catalytic subunit Esa1 (homologous to human Tip60).
    GO:0032777    Piccolo NuA4 histone acetyltransferase complex    A heterotrimeric H4/H2A histone acetyltransferase complex with a substrate preference of chromatin over free histones. It contains a subset of the proteins found in the larger NuA4 histone acetyltransferase complex; for example, the S. cerevisiae complex contains Esa1p, Yng2p, and Epl1p.
    GO:0000812    Swr1 complex    A multisubunit protein complex that is involved in chromatin remodeling. It is required for the incorporation of the histone variant H2AZ into chromatin. In S. cerevisiae, the complex contains Swr1p, a Swi2/Snf2-related ATPase, and 12 additional subunits.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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.

 Visualization

(-) Interactive Views

NMR Structure
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1x4i)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1x4i
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  ING3_HUMAN | Q9NXR8
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  ING3_HUMAN | Q9NXR8
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1X4I)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1X4I)