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(-) Description

Title :  SOLUTION STRUCTURE OF THE N-TERMINAL KH DOMAIN OF HUMAN FXR1
 
Authors :  T. Nagata, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  19 May 05  (Deposition) - 19 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  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 :  T. Nagata, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama
Solution Structure Of The N-Terminal Kh Domain Of Human Fxr1
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FRAGILE X MENTAL RETARDATION SYNDROME RELATED PROTEIN 1, ISOFORM B'
    ChainsA
    EngineeredYES
    Expression System PlasmidP040621-02
    Expression System Vector TypePLASMID
    FragmentKH DOMAIN
    GeneFXR1
    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 2CPQ)

(-) Sites  (0, 0)

(no "Site" information available for 2CPQ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

NMR Structure (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_036050A233TFXR1_HUMANUnclassified  ---AA233T
2CancerSNPVAR_FXR1_HUMAN_CCDS3238_1_01 *A233TFXR1_HUMANDisease (Breast cancer)  ---AA233T
   * ID not provided by source

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

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KH_TYPE_1PS50084 Type-1 KH domain profile.FXR1_HUMAN218-279
281-351
  2A:218-279
A:281-295

(-) Exons   (5, 5)

NMR Structure (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3aENST000003575593aENSE00001862123chr3:180630090-180630524435FXR1_HUMAN1-17170--
1.8bENST000003575598bENSE00001730554chr3:180651122-18065117453FXR1_HUMAN18-35180--
1.9bENST000003575599bENSE00001708989chr3:180652926-18065301994FXR1_HUMAN35-66320--
1.10aENST0000035755910aENSE00001639975chr3:180665653-18066572472FXR1_HUMAN67-90240--
1.11ENST0000035755911ENSE00000780635chr3:180666135-180666283149FXR1_HUMAN91-140500--
1.12cENST0000035755912cENSE00000780636chr3:180666509-18066660294FXR1_HUMAN140-171321A:205-2062
1.13dENST0000035755913dENSE00000780637chr3:180667015-180667131117FXR1_HUMAN172-210391A:207-2115
1.14aENST0000035755914aENSE00000780638chr3:180669086-180669256171FXR1_HUMAN211-267571A:212-26756
1.15aENST0000035755915aENSE00000780639chr3:180671550-18067162879FXR1_HUMAN268-294271A:268-29023
1.16cENST0000035755916cENSE00000780640chr3:180675607-180675716110FXR1_HUMAN294-330371A:291-295 (gaps)15
1.17ENST0000035755917ENSE00000780641chr3:180679256-18067934287FXR1_HUMAN331-359290--
1.18aENST0000035755918aENSE00000795164chr3:180680671-18068072858FXR1_HUMAN360-379200--
1.18dENST0000035755918dENSE00001127668chr3:180680816-18068087863FXR1_HUMAN379-400220--
1.19aENST0000035755919aENSE00000780643chr3:180685839-180686042204FXR1_HUMAN400-468690--
1.20aENST0000035755920aENSE00000780644chr3:180687946-180688146201FXR1_HUMAN468-535680--
1.22ENST0000035755922ENSE00000780645chr3:180693101-18069319292FXR1_HUMAN535-565310--
1.23iENST0000035755923iENSE00001920434chr3:180693910-1806949501041FXR1_HUMAN566-621560--

(-) 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:91
 aligned with FXR1_HUMAN | P51114 from UniProtKB/Swiss-Prot  Length:621

    Alignment length:158
                                   164       174       184       194       204       214       224       234       244       254       264       274       284       294       304        
           FXR1_HUMAN   155 GACRIFYHPETTQLMILSASEATVKRVNILSDMHLRSIRTKLMLMSRNEEATKHLECTKQLAAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDTGTFRIYGESADAVKKARGFLEFVEDFIQVPRNLVGKVIGKNGKVIQEIVDKSG 312
               SCOP domains ---------------------------------------------------------d2cpqa1 A:212-289                                                             ----------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..---------------.....-----------------------------------.......eeeeee....hhhhhh....hhhhhhh....eeeeeee....eeeeee..hhhhhhhh..............-------...----------.. Sec.struct. author
             SAPs(SNPs) (1) ------------------------------------------------------------------------------T------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------------------------------------------------T------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ---------------------------------------------------------------KH_TYPE_1  PDB: A:218-279 UniProt: 218-279                    -KH_TYPE_1  PDB: A:281-295        PROSITE
           Transcript 1 (1) Exon 1.12c       Exon 1.13d  PDB: A:207-211 [INCOMPLETE]Exon 1.14a  PDB: A:212-267 UniProt: 211-267 [INCOMPLETE] Exon 1.15a  PDB: A:268-290 ------------------ Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------------------------------------Exon 1.16c          Transcript 1 (2)
                 2cpq A 205 GS---------------SGSSG-----------------------------------TKQLAAAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDTGTFRIYGESADAVKKARGFLEFVEDFIQVPS-------GPS----------SG 295
                             |       -       209 |       -         -         -       214       224       234       244       254       264       274       284     |   -   | |   -      | 
                             |             207 211                                 212                                                                           290     291 |        294 
                           206                                                                                                                                             293            

   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 2CPQ)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (26, 26)

NMR Structure(hide GO term definitions)
Chain A   (FXR1_HUMAN | P51114)
molecular function
    GO:0002151    G-quadruplex RNA binding    Interacting selectively and non-covalently with G-quadruplex RNA structures, in which groups of four guanines adopt a flat, cyclic hydrogen-bonding arrangement known as a guanine tetrad.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0033592    RNA strand annealing activity    Facilitates the base-pairing of complementary single-stranded RNA.
    GO:0003730    mRNA 3'-UTR binding    Interacting selectively and non-covalently with the 3' untranslated region of an mRNA molecule.
    GO:0003729    mRNA binding    Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
    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:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    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:0007517    muscle organ development    The process whose specific outcome is the progression of the muscle over time, from its formation to the mature structure. The muscle is an organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work.
    GO:0017148    negative regulation of translation    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:2000637    positive regulation of gene silencing by miRNA    Any process that activates or increases the frequency, rate or extent of gene silencing by miRNA.
cellular component
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    GO:0043034    costamere    Regular periodic sub membranous arrays of vinculin in skeletal and cardiac muscle cells, these arrays link Z-discs to the sarcolemma and are associated with links to extracellular matrix.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    GO:0043197    dendritic spine    A small, membranous protrusion from a dendrite that forms a postsynaptic compartment - typically receiving input from a single presynapse. They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable including "thin", "stubby", "mushroom", and "branched", with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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: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.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0005844    polysome    A multiribosomal structure representing a linear array of ribosomes held together by messenger RNA. They represent the active complexes in cellular protein synthesis and are able to incorporate amino acids into polypeptides both in vivo and in vitro.
    GO:0035770    ribonucleoprotein granule    A non-membranous macromolecular complex containing proteins and translationally silenced mRNAs. RNA granules contain proteins that control the localization, stability, and translation of their RNA cargo. Different types of RNA granules (RGs) exist, depending on the cell type and cellular conditions.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FXR1_HUMAN | P511143kuf 3o8v

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