1B7F | PR0011 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   SXL-LETHAL PROTEIN/RNA COMPLEX

Authors :   N. Handa, O. Nureki, K. Kurimoto, I. Kim, H. Sakamoto, Y. Shimura, Y. Mut S. Yokoyama, Riken Structural Genomics/Proteomics Initiative

Date :   23 Jan 99 (Deposition) - 03 May 99 (Release) - 28 Dec 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym. Unit : A,B,P,Q
Biol. Unit 1: A,P  (1x)
Biol. Unit 2: B,Q  (1x)

Keywords :   Splicing Regulation, Rnp Domain, Rna Complex, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Rna- Binding Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Handa, O. Nureki, K. Kurimoto, I. Kim, H. Sakamoto, Y. Shimura, Y. Muto, S. Yokoyama
Structural Basis For Recognition Of The Tra Mrna Precursor By The Sex-Lethal Protein.
Nature V. 398 579 1999
PubMed-ID: 10217141 | Reference-DOI: 10.1038/19242

*Molecule 1 - RNA (5'-R(PGPUPUPGPUPUPUPUPUPUPUPU)-3')*
	Chains	:	P, Q
	Engineered	:	YES
	Other Details	:	ORIGIN OF THE SEQUENCE: DROSOPHILA MELANOGASTER, NUCLEUS
	Synonym	:	TRA PRE-MRNA
	Synthetic	:	YES

Molecule 2 - PROTEIN (SXL-LETHAL PROTEIN)
	Cellular Location	:	NUCLEUS
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PK7
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	2 RNP-DOMAINS
	Mutation	:	YES
	Organism Common	:	FRUIT FLY
	Organism Scientific	:	DROSOPHILA MELANOGASTER
	Organism Taxid	:	7227

		1	2	3	4
Asymmetric Unit	:	A	B	P	Q
Biological Unit 1 (1x)	:	A		P
Biological Unit 2 (1x)	:		B		Q

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1B7F)

(no "Site" information available for 1B7F)

(no "SS Bond" information available for 1B7F)

(no "Cis Peptide Bond" information available for 1B7F)

(no "SAP(SNP)/Variant" information available for 1B7F)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	SXL_DROME	125-203 211-291	4	A:125-203 B:125-203 A:211-289 B:211-289

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	SXL_DROME	125-203 211-291	2	A:125-203 - A:211-289 -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	SXL_DROME	125-203 211-291	2	- B:125-203 - B:211-289

(no "Exon" information available for 1B7F)

Asymmetric Unit

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:167
 aligned with SXL_DROME | P19339 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:167
                                   132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       
            SXL_DROME   123 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSFGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 289
               SCOP domains d1b7fa1 A:123-204 Sex-lethal protein                                              d1b7fa2 A:205-289 Sex-lethal protein                                                  SCOP domains
               CATH domains ----1b7fA01 A:127-197  [code=3.30.70.330, no name defined]                 ---------------1b7fA02 A:213-289  [code=3.30.70.330, no name defined]                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.......hhhhhhhhh....eeeee............eeeeee..hhhhhhhhhhh..........eeee...........eeeee.......hhhhhhhh.....eeeeee............eeeee..hhhhhhhhhhh............eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --RRM  PDB: A:125-203 UniProt: 125-203                                           -------RRM  PDB: A:211-289 UniProt: 211-291                                            PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b7f A 123 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 289
                                   132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282

Chain B from PDB  Type:PROTEIN  Length:167
 aligned with SXL_DROME | P19339 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:167
                                   132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       
            SXL_DROME   123 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSFGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 289
               SCOP domains d1b7fb1 B:123-204 Sex-lethal protein                                              d1b7fb2 B:205-289 Sex-lethal protein                                                  SCOP domains
               CATH domains ----1b7fB01 B:127-197  [code=3.30.70.330, no name defined]                 ---------------1b7fB02 B:213-289  [code=3.30.70.330, no name defined]                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.......hhhhhhhhh....eeeee............eeeeee..hhhhhhhhhhh..........eeee...........eeeee.......hhhhhhhh.....eeeeee............eeeee..hhhhhhhhhhh............eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --RRM  PDB: B:125-203 UniProt: 125-203                                           -------RRM  PDB: B:211-289 UniProt: 211-291                                            PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b7f B 123 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 289
                                   132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282

Chain P from PDB  Type:RNA  Length:12
                                            
                 1b7f P   1 GUUGUUUUUUUU  12
                                    10

Chain Q from PDB  Type:RNA  Length:12
                                            
                 1b7f Q   1 GUUGUUUUUUUU  12
                                    10

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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Ferredoxin-like (1795)

Superfamily: RNA-binding domain, RBD (289)

Family: Canonical RBD (214)

Protein domain: Sex-lethal protein (4)

Fruit fly (Drosophila melanogaster) [TaxId: 7227] (4)

1a	d1b7fa1	A:123-204
1b	d1b7fa2	A:205-289
1c	d1b7fb1	B:123-204
1d	d1b7fb2	B:205-289

Asymmetric Unit

Classes(

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Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.330, no name defined] (307)

[unclassified] (45)

1a	1b7fA02	A:213-289
1b	1b7fB02	B:213-289
1c	1b7fA01	A:127-197
1d	1b7fB01	B:127-197

(no "Pfam Domain" information available for 1B7F)

Asymmetric Unit(hide GO term definitions)

Chain A,B (SXL_DROME | P19339)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0008083	growth factor activity	The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
	GO:0003730	mRNA 3'-UTR binding	Interacting selectively and non-covalently with the 3' untranslated region of an mRNA molecule.
	GO:0048027	mRNA 5'-UTR binding	Interacting selectively and non-covalently with the 5' 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: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:0008266	poly(U) RNA binding	Interacting selectively and non-covalently with a sequence of uracil residues in an RNA molecule.
	GO:0008187	poly-pyrimidine tract binding	Interacting selectively and non-covalently with any stretch of pyrimidines (cytosine or uracil) in an RNA molecule.
	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:0000900	translation repressor activity, nucleic acid binding	Antagonizes the ribosome-mediated translation of mRNA into a polypeptide via direct binding (through a selective and non-covalent interaction) to nucleic acid.
biological process
	GO:0000380	alternative mRNA splicing, via spliceosome	The process of generating multiple mRNA molecules from a given set of exons by differential use of exons from the primary transcript(s) to form multiple mature mRNAs that vary in their exon composition.
	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:0007549	dosage compensation	Compensating for the variation in the unpaired sex chromosome:autosome chromosome ratios between sexes by activation or inactivation of genes on one or both of the sex chromosomes.
	GO:0019099	female germ-line sex determination	The determination of sex and sexual phenotype in a female organism's germ line.
	GO:0030237	female sex determination	The specification of female sex of an individual organism.
	GO:0019101	female somatic sex determination	The determination of sex and sexual phenotypes in a female organism's soma.
	GO:0007281	germ cell development	The process whose specific outcome is the progression of an immature germ cell over time, from its formation to the mature structure (gamete). A germ cell is any reproductive cell in a multicellular organism.
	GO:0007446	imaginal disc growth	The increase in mass of imaginal discs by cell proliferation prior to metamorphosis. Imaginal discs are epithelial infoldings in the larvae of holometabolous insects that develop into adult structures (legs, antennae, wings, etc.) during metamorphosis from larval to adult form.
	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:0048025	negative regulation of mRNA splicing, via spliceosome	Any process that stops, prevents or reduces the rate or extent of mRNA splicing via a spliceosomal mechanism.
	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:0009994	oocyte differentiation	The process in which a relatively unspecialized immature germ cell acquires the specialized features of a mature female gamete.
	GO:0048477	oogenesis	The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster.
	GO:0007131	reciprocal meiotic recombination	The cell cycle process in which double strand breaks are formed and repaired through a double Holliday junction intermediate. This results in the equal exchange of genetic material between non-sister chromatids in a pair of homologous chromosomes. These reciprocal recombinant products ensure the proper segregation of homologous chromosomes during meiosis I and create genetic diversity.
	GO:0000381	regulation of alternative mRNA splicing, via spliceosome	Any process that modulates the frequency, rate or extent of alternative splicing of nuclear mRNAs.
	GO:0048024	regulation of mRNA splicing, via spliceosome	Any process that modulates the frequency, rate or extent of mRNA splicing via a spliceosomal mechanism.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0007530	sex determination	Any process that establishes and transmits the specification of sexual status of an individual organism.
	GO:0007541	sex determination, primary response to X:A ratio	The developmental process in which an organism interprets its X to autosomal chromosomal complement.
	GO:0007548	sex differentiation	The establishment of the sex of an organism by physical differentiation.
	GO:0007224	smoothened signaling pathway	A series of molecular signals generated as a consequence of activation of the transmembrane protein Smoothened.
	GO:0018993	somatic sex determination	The determination of sex and sexual phenotypes in an organism's soma.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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	1b7f
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	SXL_DROME \| P19339	:	1sxl 2sxl 3sxl 4qqb

(no "Related Entries Specified in the PDB File" available for 1B7F)

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