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(-) Description

Title :  SOLUTION NMR STRUCTURE OF CAPER RRM2 DOMAIN. NORTHEAST STRUCTURAL GENOMICS TARGET HR4730A
 
Authors :  P. Rossi, L. Zhao, C. Nwosu, K. Cunningham, L. Owens, R. Xiao, J. Liu, M. C. Baran, G. Swapna, T. B. Acton, B. Rost, G. T. Montelione, Northeast Structural Genomics Consortium (Nesg)
Date :  28 Jun 07  (Deposition) - 04 Sep 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Rna Binding Motif Of Rbm39_human (Caper), Rrm2 Domain, Solution Nmr Structure, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Rossi, R. Xiao, T. B. Acton, G. T. Montelione
Solution Nmr Structure Of Caper Rrm2 Domain.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RNA-BINDING PROTEIN 39
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15
    Expression System StrainBL21(DE3)+MAGIC
    Expression System Taxid562
    Expression System VectorHR4730A-15.1
    Expression System Vector TypePLASMID
    FragmentRRM2 DOMAIN: RESIDUES 235-331
    GeneRBM39, HCC1, RNPC2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRNA-BINDING MOTIF PROTEIN 39, RNA-BINDING REGION- CONTAINING PROTEIN 2, HEPATOCELLULAR CARCINOMA PROTEIN 1, SPLICING FACTOR HCC1

 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 2JRS)

(-) Sites  (0, 0)

(no "Site" information available for 2JRS)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.RBM39_HUMAN250-328
153-230
  1A:27-105
-

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1qENST000002533631qENSE00001938005chr20:34329873-3432986311RBM39_HUMAN-00--
1.3aENST000002533633aENSE00002165663chr20:34328809-3432874664RBM39_HUMAN1-17170--
1.3mENST000002533633mENSE00001659166chr20:34326939-3432689050RBM39_HUMAN18-34170--
1.7eENST000002533637eENSE00002169946chr20:34320057-34319863195RBM39_HUMAN34-99660--
1.8cENST000002533638cENSE00001633700chr20:34317449-3431738466RBM39_HUMAN99-121230--
1.9aENST000002533639aENSE00001644239chr20:34317287-3431723454RBM39_HUMAN121-139190--
1.10cENST0000025336310cENSE00001789378chr20:34313077-34312960118RBM39_HUMAN139-178400--
1.11cENST0000025336311cENSE00002082263chr20:34312644-34312492153RBM39_HUMAN179-229511A:1-6 (gaps)11
1.12bENST0000025336312bENSE00001773401chr20:34309799-34309662138RBM39_HUMAN230-275461A:7-5246
1.13aENST0000025336313aENSE00001613700chr20:34304727-3430466266RBM39_HUMAN276-297221A:53-7422
1.14aENST0000025336314aENSE00001623326chr20:34302311-34302107205RBM39_HUMAN298-366691A:75-10834
1.16eENST0000025336316eENSE00001600583chr20:34301018-3430094178RBM39_HUMAN366-392270--
1.18bENST0000025336318bENSE00001753743chr20:34297196-3429714651RBM39_HUMAN392-409180--
1.19dENST0000025336319dENSE00001693917chr20:34295123-3429504282RBM39_HUMAN409-436280--
1.20cENST0000025336320cENSE00001670308chr20:34293252-34293147106RBM39_HUMAN436-471360--
1.20fENST0000025336320fENSE00001598280chr20:34292668-3429259079RBM39_HUMAN472-498270--
1.21hENST0000025336321hENSE00001887140chr20:34292503-34291532972RBM39_HUMAN498-530330--

(-) 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:108
 aligned with RBM39_HUMAN | Q14498 from UniProtKB/Swiss-Prot  Length:530

    Alignment length:113
                                   228       238       248       258       268       278       288       298       308       318       328   
          RBM39_HUMAN   219 LGVPIIVQASQAEKNRAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERTD 331
               SCOP domains ----------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -----------------------------2jrsA01 A:25-103  [code=3.30.70.330, no name defined]                          ----- CATH domains
               Pfam domains ---------------------------------RRM_1-2jrsA01 A:29-99                                                  --------- Pfam domains
         Sec.struct. author ..-----........................eeeeee......hhhhhhhhhh....eeeeeeee......eeeeeeeee.hhhhhhhhhhhhh.........eee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RRM  PDB: - -------------------RRM  PDB: A:27-105 UniProt: 250-328                                            --- PROSITE
               Transcript 1 Exon 1.11c Exon 1.12b  PDB: A:7-52 UniProt: 230-275      Exon 1.13a            Exon 1.14a  PDB: A:75-108          Transcript 1
                 2jrs A   1 MG-----HHHHHHSHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERTD 108
                             |     | 5        15        25        35        45        55        65        75        85        95       105   
                             2     3                                                                                                         

   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  (0, 0)

(no "SCOP Domain" information available for 2JRS)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: RRM (206)

(-) Gene Ontology  (14, 14)

NMR Structure(hide GO term definitions)
Chain A   (RBM39_HUMAN | Q14498)
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.
    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).
biological process
    GO:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    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: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: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.
cellular component
    GO:0015630    microtubule cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins.
    GO:0005815    microtubule organizing center    An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
    GO:0016607    nuclear speck    A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
    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
        RBM39_HUMAN | Q144982mhn 4oo6 4oz0 4oz1 4yud

(-) Related Entries Specified in the PDB File

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