2RRA - JenaLib

Title :   SOLUTION STRUCTURE OF RNA BINDING DOMAIN IN HUMAN TRA2 BETA PROTEIN IN COMPLEX WITH RNA (GAAGAA)

Authors :   K. Tsuda, K. Kuwasako, M. Takahashi, T. Someya, M. Inoue, T. Kigawa, T. T M. Shirouzu, S. Sugano, Y. Muto, S. Yokoyama

Date :   17 Jun 10 (Deposition) - 27 Apr 11 (Release) - 27 Apr 11 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (20x)
NMR Structure *: A,B  (1x)

Keywords :   Rrm Domain, Rbd, Protein-Rna Complex, Rna Binding Protein-Rna Complex, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Tsuda, T. Someya, K. Kuwasako, M. Takahashi, F. He, S. Unzai, M. Inoue, T. Harada, S. Watanabe, T. Terada, N. Kobayashi, M. Shirouzu T. Kigawa, A. Tanaka, S. Sugano, P. Guntert, S. Yokoyama, Y. Muto
Structural Basis For The Dual Rna-Recognition Modes Of Huma Tra2-Beta Rrm.
Nucleic Acids Res. V. 39 1538 2011
PubMed-ID: 20926394 | Reference-DOI: 10.1093/NAR/GKQ854

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

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:99
 aligned with Q8N1H4_HUMAN | Q8N1H4 from UniProtKB/TrEMBL  Length:252

    Alignment length:145
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160     
         Q8N1H4_HUMAN    21 GSAHGSGKSARHTPAKSRSRSHRRSRSRSYSRDYRRRHSHSHSPMSTRRRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRPHT 165
               SCOP domains d2   rraa                                           _ A: automated matches                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------RRM_1-2rraA01 A:120-190                                                ----------- Pfam domains
         Sec.struct. author ..---....-------------------------------------------..........eeeee......hhhhhhhhhhhhh.eeeeeeee......eeeeeeeee.hhhhhhhhhhhhh..ee..ee.eeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rra A 103 GS---SGSS-------------------------------------------GNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRPHT 201
                             |   |  |-         -         -         -         -  |    116       126       136       146       156       166       176       186       196     
                             | 105  |                                         109                                                                                            
                           104    108

Chain A from PDB  Type:PROTEIN  Length:99
 aligned with TRA2B_HUMAN | P62995 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:181
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 
          TRA2B_HUMAN    21 GSAHGSGKSARHTPARSRSKEDSRRSRSKSRSRSESRSRSRRSSRRHYTRSRSRSRSHRRSRSRSYSRDYRRRHSHSHSPMSTRRRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRPHT 201
               SCOP domains d2   rr                                   aa                                            _ A: automated matches                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------RRM_1-2rraA01 A:120-190                                                ----------- Pfam domains
         Sec.struct. author ..---..-----------------------------------..--------------------------------------------..........eeeee......hhhhhhhhhhhhh.eeeeeeee......eeeeeeeee.hhhhhhhhhhhhh..ee..ee.eeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------RRM  PDB: A:118-196 UniProt: 118-196                                           ----- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rra A 103 GS---SG-----------------------------------SS--------------------------------------------GNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRPHT 201
                             |   ||  -         -         -         -  ||     -         -         -         -       110       120       130       140       150       160       170       180       190       200 
                           104 105|                                 107|                                          109                                                                                            
                                106                                  108

Chain B from PDB  Type:RNA  Length:6
                                      
                 2rra B   1 GAAGAA   6

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)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (14, 16)

NMR Structure(hide GO term definitions)

Chain A (TRA2B_HUMAN | P62995)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	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: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: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:0021796	cerebral cortex regionalization	The regionalization process that results in the creation of areas within the cerebral cortex that will direct the behavior of cell migration and differentiation as the cortex develops.
	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: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:0048026	positive regulation of mRNA splicing, via spliceosome	Any process that activates or increases the rate or extent of mRNA splicing via a spliceosomal mechanism.
	GO:0000381	regulation of alternative mRNA splicing, via spliceosome	Any process that modulates the frequency, rate or extent of alternative splicing of nuclear mRNAs.
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.

Chain A (Q8N1H4_HUMAN | Q8N1H4)

molecular function
	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.

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