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(-) Description

Title :  SOLUTION NMR STRUCTURE OF THE FIRST DOMAIN OF KSRP
 
Authors :  I. Diaz-Moreno, A. Ramos, M. F. Garcia-Mayoral, D. Hollingworth
Date :  30 Jan 07  (Deposition) - 26 Feb 08  (Release) - 17 Mar 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (25x)
Keywords :  Kh Domain, Rna Binding Protein, Ksrp (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Diaz-Moreno, D. Hollingworth, T. A. Frenkiel, G. Kelly, S. Martin, S. Howell, M. Garcia-Mayoral, R. Gherzi, P. Briata, A. Ramos
Phosphorylation-Mediated Unfolding Of A Kh Domain Regulates Ksrp Localization Via 14-3-3 Binding.
Nat. Struct. Mol. Biol. V. 16 238 2009
PubMed-ID: 19198587  |  Reference-DOI: 10.1038/NSMB.1558
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - KHSRP PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGEX-JDK
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: KH DOMAIN
    Gene: KHSRP
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: KH1 DOMAIN OF K-HOMOLOGY SPLICING RECOGNITION PROTEIN

 Structural Features

(-) Chains, Units

  
NMR Structure (25x): 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2OPU)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KH_TYPE_1PS50084 Type-1 KH domain profile.FUBP2_HUMAN144-208
233-299
322-386
424-491		  1A:19-83
-
-
-

(-) Exons   (5, 5)

NMR Structure (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003981481aENSE00001561079chr19:6424822-6424464359FUBP2_HUMAN1-83830--
1.2ENST000003981482ENSE00001160298chr19:6422447-642235197FUBP2_HUMAN84-116330--
1.3ENST000003981483ENSE00001160287chr19:6421699-642166139FUBP2_HUMAN116-129140--
1.4ENST000003981484ENSE00001160276chr19:6421328-642128940FUBP2_HUMAN129-142141A:5-1713
1.5ENST000003981485ENSE00001160266chr19:6420482-642043350FUBP2_HUMAN142-159181A:17-3418
1.6ENST000003981486ENSE00001160257chr19:6420155-642008472FUBP2_HUMAN159-183251A:34-5825
1.7ENST000003981487ENSE00001160249chr19:6419271-641921458FUBP2_HUMAN183-202201A:58-7720
1.8ENST000003981488ENSE00001160243chr19:6418887-6418713175FUBP2_HUMAN202-260591A:77-9317
1.9ENST000003981489ENSE00001160234chr19:6418592-641849499FUBP2_HUMAN261-293330--
1.10ENST0000039814810ENSE00001160227chr19:6418090-641799299FUBP2_HUMAN294-326330--
1.11ENST0000039814811ENSE00001160220chr19:6417852-6417750103FUBP2_HUMAN327-361350--
1.12bENST0000039814812bENSE00001160213chr19:6417098-6416998101FUBP2_HUMAN361-394340--
1.13ENST0000039814813ENSE00001160204chr19:6416893-6416749145FUBP2_HUMAN395-443490--
1.14ENST0000039814814ENSE00001160198chr19:6416661-6416501161FUBP2_HUMAN443-496540--
1.15ENST0000039814815ENSE00001160189chr19:6416418-6416309110FUBP2_HUMAN497-533370--
1.16ENST0000039814816ENSE00001160181chr19:6415907-641581989FUBP2_HUMAN533-563310--
1.17ENST0000039814817ENSE00001160174chr19:6415745-6415545201FUBP2_HUMAN563-630680--
1.18ENST0000039814818ENSE00001060055chr19:6415468-641539178FUBP2_HUMAN630-656270--
1.19bENST0000039814819bENSE00001531832chr19:6415312-6415152161FUBP2_HUMAN656-709540--
1.22aENST0000039814822aENSE00001531829chr19:6414131-64131211011FUBP2_HUMAN710-71120--

(-) 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:89
 aligned with FUBP2_HUMAN | Q92945 from UniProtKB/Swiss-Prot  Length:711

    Alignment length:89
                                   139       149       159       169       179       189       199       209         
          FUBP2_HUMAN   130 ISSQLGPIHPPPRTSMTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPESVQKAKMMLDDIVSRGRGG 218
               SCOP domains d2opua_ A: automated matches                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------KH_1-2opuA01 A:21-83                                           ---------- Pfam domains
         Sec.struct. author ..eee.....hhhhhheeeeeehhhhhhhhh...hhhhhhhhhhhh...eee........eeeee..hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------KH_TYPE_1  PDB: A:19-83 UniProt: 144-208                         ---------- PROSITE
           Transcript 1 (1) Exon 1.4     ----------------Exon 1.6  PDB: A:34-58   ------------------Exon 1.8          Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.5          -----------------------Exon 1.7            ---------------- Transcript 1 (2)
                 2opu A   5 ISSQLGPIHPPPRTSMTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPESVQKAKMMLDDIVSRGRGG  93
                                    14        24        34        44        54        64        74        84
   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
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: KH (43)

(-) Gene Ontology  (23, 23)

NMR Structure(hide GO term definitions)
Chain A   (FUBP2_HUMAN | Q92945)
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: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.
biological process
    GO:0008380    RNA splicing    The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
    GO:0000375    RNA splicing, via transesterification reactions    Splicing of RNA via a series of two transesterification reactions.
    GO:0006402    mRNA catabolic process    The chemical reactions and pathways resulting in the breakdown of mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0051028    mRNA transport    The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0043488    regulation of mRNA stability    Any process that modulates the propensity of mRNA molecules to degradation. Includes processes that both stabilize and destabilize mRNAs.
    GO:2000628    regulation of miRNA metabolic process    Any process that modulates the frequency, rate or extent of miRNA metabolic process.
    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:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0010494    cytoplasmic stress granule    A dense aggregation in the cytosol composed of proteins and RNAs that appear when the cell is under stress.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    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
        FUBP2_HUMAN | Q92945: 2hh2 2hh3 2jvz 2opv 4b8t

(-) Related Entries Specified in the PDB File

2hh2 SOLUTION NMR STRUCTURE OF THE FOURTH KH DOMAIN OF KSRP
2hh3 SOLUTION NMR STRUCTURE OF THE THIRD KH DOMAIN OF KSRP