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(-) Description

Title :  SOLUTION STRUCTURE OF KH DOMAIN IN FUSE BINDING PROTEIN 1
 
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, Kh Domain, Structural Genomics, 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 :  F. He, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama
Solution Structure Of Kh Domain In Fuse Binding Protein 1
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FAR UPSTREAM ELEMENT BINDING PROTEIN 1
    Chains: A
    Engineered: YES
    Expression System Plasmid: P040802-06
    Expression System Vector Type: PLASMID
    Fragment: KH DOMAIN
    Gene: FUBP1, D3ERTD330E
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: CELL FREE PROTEIN SYNTHESIS
    Synonym: FUSE BINDING PROTEIN 1, FBP

 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 1X4N)

(-) Sites  (0, 0)

(no "Site" information available for 1X4N)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X4N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1X4N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X4N)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KH_TYPE_1PS50084 Type-1 KH domain profile.FUBP1_MOUSE96-160
181-247
271-335
372-439		  1A:14-78
-
-
-

(-) Exons   (0, 0)

(no "Exon" information available for 1X4N)

(-) 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:92
 aligned with FUBP1_MOUSE | Q91WJ8 from UniProtKB/Swiss-Prot  Length:651

    Alignment length:173
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179   
          FUBP1_MOUSE    10 PSSGSAGGGGGGVVNDAFKDALQRARQIAAKIGGDAGTSLNSNDYGYGGQKRPLEDGDQPDAKKVPPQNDSFGAQLPPMHQQQSRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIVEKGRPAPGFHHGDGPGNA 182
               SCOP domains -------------------------------------------------------------------------------d1x4 na1 A:8-86 Far upstream binding element, FBP                               -------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------KH_1-1x4nA01 A:16-78                                           ---------------------- Pfam domains
         Sec.struct. author .......------------------------------------------------------------------------....-...eeeeeeeehhhhhhhh....hhhhhhhhh...eeee........eeeeeeee.hhhhhhhhhhhhhhhhh..--------...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------KH_TYPE_1  PDB: A:14-78 UniProt: 96-160                          --------------------KH PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x4n A   1 GSSGSSG------------------------------------------------------------------------HQQQ-RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIVEKGR--------SGPSSG  92
                                  |  -         -         -         -         -         -         -         8  | |   17        27        37        47        57        67        77        |-       |89   
                                  7                                                                        8 11 |                                                                        86       87     
                                                                                                               12
   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
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1X4N)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: KH (43)

(-) Gene Ontology  (16, 16)

NMR Structure(hide GO term definitions)
Chain A   (FUBP1_MOUSE | Q91WJ8)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0001205    transcriptional activator 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 activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
biological process
    GO:0016049    cell growth    The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.
    GO:0071425    hematopoietic stem cell proliferation    The expansion of a hematopoietic stem cell population by cell division. A hematopoietic stem cell is a stem cell from which all cells of the lymphoid and myeloid lineages develop.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    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:0017145    stem cell division    The self-renewing division of a stem cell. A stem cell is an undifferentiated cell, in the embryo or adult, that can undergo unlimited division and give rise to one or several different cell types.
    GO:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    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

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UniProtKB/Swiss-Prot
        FUBP1_MOUSE | Q91WJ8: 1x4m

(-) Related Entries Specified in the PDB File

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