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(-) Description

Title :  SOLUTION STRUCTURE OF THE RRM_1 DOMAIN OF HIV TAT SPECIFIC FACTOR 1 VARIANT
 
Authors :  W. Dang, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  30 Mar 06  (Deposition) - 30 Sep 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Nmr, Structural Genomics, Rrm_1 Domain, Hiv Tat Specific Factor 1 Variant, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. Dang, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama
Solution Structure Of The Rrm_1 Domain Of Hiv Tat Specific Factor 1 Variant
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HIV TAT SPECIFIC FACTOR 1 VARIANT
    ChainsA
    EngineeredYES
    Expression SystemCELL FREE SYNTHESIS
    Expression System PlasmidP050711-19
    Expression System Vector TypePLASMID
    FragmentRRM_1 DOMAIN
    GeneHIV TAT SPECIFIC FACTOR 1 VARIANT
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL FREE PROTEIN SYNTHESIS

 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 2DIT)

(-) Sites  (0, 0)

(no "Site" information available for 2DIT)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DIT)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.HTSF1_HUMAN133-218
264-349
  1-
A:16-101

(-) Exons   (5, 5)

NMR Structure (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000002183642aENSE00001932076X:135579670-135580029360HTSF1_HUMAN1-62620--
1.3ENST000002183643ENSE00000677003X:135581757-135581937181HTSF1_HUMAN63-123610--
1.4ENST000002183644ENSE00000677004X:135582317-13558236448HTSF1_HUMAN123-139170--
1.5ENST000002183645ENSE00000677005X:135582823-135582977155HTSF1_HUMAN139-190520--
1.6bENST000002183646bENSE00002199661X:135584937-135585100164HTSF1_HUMAN191-245551A:1-66
1.7ENST000002183647ENSE00000677007X:135586523-135586622100HTSF1_HUMAN245-278341A:7-3024
1.8ENST000002183648ENSE00000677008X:135591250-13559133990HTSF1_HUMAN279-308301A:31-6030
1.9ENST000002183649ENSE00000677009X:135592241-135592378138HTSF1_HUMAN309-354461A:61-10646
1.10bENST0000021836410bENSE00001305625X:135592967-1355945051539HTSF1_HUMAN355-7554011A:107-112 (gaps)26

(-) 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:112
 aligned with HTSF1_HUMAN | O43719 from UniProtKB/Swiss-Prot  Length:755

    Alignment length:198
                                   231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411        
          HTSF1_HUMAN   222 GEYDASKKKKKCKDYKKKLSMQQKQLDWRPERRAGPSRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTTDYQVEETSREREERLRGWEAFLNAPEANRGLRRSDSVSASERAGPSRARHFSEHPSTSKMNAQETATG 419
               SCOP domains ----------------------------------d2dita1 A:8-106 HIV Tat-specific factor 1                                                          ----------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
     Sec.struct. author (1) ......---------------------------..........eeeee......hhhh..hhhhhhhhhhhhhhhh.....eeee.......----hhhhhhhhhhhhhh....ee..ee.eeee........---------------------------------------....--------------------.. Sec.struct. author (1)
     Sec.struct. author (2) --------------------------------------------------------------------------------------------eeeee----------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------RRM  PDB: A:16-101 UniProt: 264-349                                                   ---------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6b  PDB: A:1-6   ---------------------------------Exon 1.8  PDB: A:31-60        Exon 1.9  PDB: A:61-106 UniProt: 309-354      Exon 1.10b  PDB: A:107-112 (gaps) UniProt: 355-755 [INCOMPLETE]   Transcript 1 (1)
           Transcript 1 (2) -----------------------Exon 1.7  PDB: A:7-30 [INCOMPLETE]--------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2dit A   1 GSSGSS---------------------------GGPSRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTTDYQ---------------------------------------SGPS--------------------SG 112
                                 |   -         -         -   |    13        23        33        43        53        63        73        83        93       103  |      -         -         -         -  |  |   -         -      | 
                                 6                           7                                                                                                106                                     107  |                  111 
                                                                                                                                                                                                         110                      

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

NMR Structure(hide GO term definitions)
Chain A   (HTSF1_HUMAN | O43719)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0000398    mRNA splicing, via spliceosome    The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
    GO:0032784    regulation of DNA-templated transcription, elongation    Any process that modulates the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides catalyzed by a DNA-dependent RNA polymerase.
    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:0019079    viral genome replication    Any process involved directly in viral genome replication, including viral nucleotide metabolism.
cellular component
    GO:0005686    U2 snRNP    A ribonucleoprotein complex that contains small nuclear RNA U2.
    GO:0005684    U2-type spliceosomal complex    Any spliceosomal complex that forms during the splicing of a messenger RNA primary transcript to excise an intron that has canonical consensus sequences near the 5' and 3' ends.
    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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