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(-) Description

Title :  SOLUTION STRUCTURE OF RSGI RUH-066, A GTF2I DOMAIN IN HUMAN CDNA
 
Authors :  Y. Doi-Katayama, H. Hirota, T. Tomizawa, S. Koshiba, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  30 Sep 06  (Deposition) - 30 Mar 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Rsgi Ruh-066, Transcription Factor, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Doi-Katayama, H. Hirota, T. Tomizawa, S. Koshiba, T. Kigawa, S. Yokoyama
Solution Structure Of Rsgi Ruh-066, A Gtf2I Domain In Human Cdna
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GENERAL TRANSCRIPTION FACTOR II-I REPEAT DOMAIN- CONTAINING PROTEIN 1
    ChainsA
    EngineeredYES
    Expression System PlasmidP050627-06
    Expression System Vector TypePLASMID
    FragmentGTF2I DOMAIN, GTF2I-LIKE 3
    GeneNP005676
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS (E. COLI)
    SynonymGTF2I REPEAT DOMAIN-CONTAINING PROTEIN 1, MUSCLE TFII-I REPEAT DOMAIN-CONTAINING PROTEIN 1, GENERAL TRANSCRIPTION FACTOR III, SLOW- MUSCLE-FIBER ENHANCER- BINDING PROTEIN, USE B1-BINDING PROTEIN, MUSTRD1/BEN, WILLIAMS-BEUREN SYNDROME CHROMOSOME REGION 11 PROTEIN

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2DZQ)

(-) Sites  (0, 0)

(no "Site" information available for 2DZQ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_013446M652VGT2D1_HUMANPolymorphism2301895AG95V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GTF2IPS51139 GTF2I-like repeat profile.GT2D1_HUMAN119-213
342-436
556-650
696-790
793-887
  1-
-
A:8-93
-
-

(-) Exons   (6, 6)

NMR Structure (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002657551aENSE00001341217chr7:73868120-73868506387GT2D1_HUMAN-00--
1.3ENST000002657553ENSE00002196204chr7:73922405-73922533129GT2D1_HUMAN1-41410--
1.4ENST000002657554ENSE00000691482chr7:73927160-73927301142GT2D1_HUMAN42-89480--
1.5bENST000002657555bENSE00000691481chr7:73929771-73929926156GT2D1_HUMAN89-141530--
1.6ENST000002657556ENSE00000403997chr7:73932469-73932652184GT2D1_HUMAN141-202620--
1.7ENST000002657557ENSE00000691478chr7:73933739-73934049311GT2D1_HUMAN202-3061050--
1.8ENST000002657558ENSE00000403999chr7:73935538-7393562790GT2D1_HUMAN306-336310--
1.9ENST000002657559ENSE00000404000chr7:73938401-7393848484GT2D1_HUMAN336-364290--
1.10ENST0000026575510ENSE00000404001chr7:73944064-73944247184GT2D1_HUMAN364-425620--
1.11ENST0000026575511ENSE00001039150chr7:73949443-7394946826GT2D1_HUMAN425-434100--
1.12ENST0000026575512ENSE00000843247chr7:73950497-73950605109GT2D1_HUMAN434-470370--
1.13ENST0000026575513ENSE00001735710chr7:73952466-7395250338GT2D1_HUMAN470-483141A:1-11
1.14ENST0000026575514ENSE00000691417chr7:73953010-7395309081GT2D1_HUMAN483-510281A:1-77
1.15ENST0000026575515ENSE00001713711chr7:73954209-7395429890GT2D1_HUMAN510-540310--
1.16ENST0000026575516ENSE00001704452chr7:73959085-7395913248GT2D1_HUMAN540-556170--
1.17aENST0000026575517aENSE00001603168chr7:73960074-7396013966GT2D1_HUMAN556-578231A:8-2114
1.18ENST0000026575518ENSE00001801491chr7:73961433-73961616184GT2D1_HUMAN578-639621A:21-8262
1.19ENST0000026575519ENSE00001716575chr7:73969504-7396955350GT2D1_HUMAN639-656181A:82-9918
1.20aENST0000026575520aENSE00001147974chr7:73969723-73969824102GT2D1_HUMAN656-690351A:99-991
1.21ENST0000026575521ENSE00000691369chr7:73971969-7397205284GT2D1_HUMAN690-718290--
1.22ENST0000026575522ENSE00000691365chr7:73973191-73973374184GT2D1_HUMAN718-779620--
1.23aENST0000026575523aENSE00001039134chr7:73973957-7397398529GT2D1_HUMAN779-789110--
1.24ENST0000026575524ENSE00001147952chr7:74004180-7400425778GT2D1_HUMAN789-815270--
1.25ENST0000026575525ENSE00000404019chr7:74005154-74005346193GT2D1_HUMAN815-879650--
1.26ENST0000026575526ENSE00001039136chr7:74009341-7400937838GT2D1_HUMAN879-892140--
1.27cENST0000026575527cENSE00000691312chr7:74015371-74015507137GT2D1_HUMAN892-937460--
1.27fENST0000026575527fENSE00001882339chr7:74016692-74016917226GT2D1_HUMAN938-959220--

(-) 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:99
 aligned with GT2D1_HUMAN | Q9UHL9 from UniProtKB/Swiss-Prot  Length:959

    Alignment length:174
                                   492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652    
          GT2D1_HUMAN   483 GTSGELGGLRPIKIEPEDLDIIQVTVPDPSPTSEEMTDSMPGHLPSEDSGYGMEMLTDKGLSEDARPEERPVEDSHGDVIRPLRKQVELLFNTRYAKAIGISEPVKVPYSKFLMHPEELFVVGLPEGISLRRPNCFGIAKLRKILEASNSIQFVIKRPELLTEGVKEPIMDSQG 656
               SCOP domains d2dzqa_                                                                            A: automated matches                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......---------------------------------------------------------------------------hhhhhhhhhhhhhhhhh.........hhhhhh....eeee................hhhhhhhh.....eeee................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------V---- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------GTF2I  PDB: A:8-93 UniProt: 556-650                                                            ------ PROSITE
           Transcript 1 (1) 1--------------------------Exon 1.15  PDB: -              ---------------Exon 1.17a  PDB: A:8-21------------------------------------------------------------Exon 1.19          Transcript 1 (1)
           Transcript 1 (2) Exon 1.14  PDB: A:1-7       -----------------------------Exon 1.16  PDB: ----------------------Exon 1.18  PDB: A:21-82 UniProt: 578-639                      ----------------1 Transcript 1 (2)
                 2dzq A   1 GSSGSSG---------------------------------------------------------------------------LRKQVELLFNTRYAKAIGISEPVKVPYSKFLMHPEELFVVGLPEGISLRRPNCFGIAKLRKILEASNSIQFVIKRPELLTEGVKEPSGPSSG  99
                                  |  -         -         -         -         -         -         -         -  |     15        25        35        45        55        65        75        85        95    
                                  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  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DZQ)

(-) Gene Ontology  (12, 12)

NMR Structure(hide GO term definitions)
Chain A   (GT2D1_HUMAN | Q9UHL9)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000981    RNA polymerase II transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0003705    transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in a distal enhancer region for RNA polymerase II (RNAP II) in order to modulate transcription by RNAP II.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    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.
    GO:0014886    transition between slow and fast fiber    The process of conversion of slow-contracting muscle fibers to a faster character. This may involve increasing of contractile rate, fast myosin gene induction, increase in glycolytic metabolic properties, altered electrophysiology and altered innervation. This process also regulates skeletal muscle adapatation.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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
        GT2D1_HUMAN | Q9UHL92d99 2dn5 2dzr

(-) Related Entries Specified in the PDB File

2d99 OTHER DOMAIN(RSGI RUH-048) FROM THE SAME PROTEIN RELATED ID: HSO002000922.2 RELATED DB: TARGETDB
2dn5 OTHER DOMAIN(RSGI RUH-057) FROM THE SAME PROTEIN
2dzr OTHER DOMAIN(RSGI RUH-067) FROM THE SAME PROTEIN