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(-) Description

Title :  STRUCTURE OF THE CORE ASAP COMPLEX
 
Authors :  A. G. Murachelli, J. Ebert, C. Basquin, H. Le Hir, E. Conti
Date :  21 Nov 11  (Deposition) - 07 Mar 12  (Release) - 18 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Transcription, Splicing, Rna Processing, Nonsense Mediated Decay, Nmd, Hdac, Histone Deacetylation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. G. Murachelli, J. Ebert, C. Basquin, H. Le Hir, E. Conti
The Structure Of The Asap Core Complex Reveals The Existence Of A Pinin-Containing Psap Complex
Nat. Struct. Mol. Biol. V. 19 378 2012
PubMed-ID: 22388736  |  Reference-DOI: 10.1038/NSMB.2242

(-) Compounds

Molecule 1 - RNA-BINDING PROTEIN WITH SERINE-RICH DOMAIN 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET SERIES
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Fragment: RRM DOMAIN, RESIDUES 122-207
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: RNPS1, SR-RELATED PROTEIN LDC2
 
Molecule 2 - HOOK-LIKE, ISOFORM A
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET SERIES
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Fragment: RSB DOMAIN, RESIDUES 648-687
    Organism Common: HUMAN FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Synonym: ACINUS, HOOK-LIKE, ISOFORM B, LD23757P
 
Molecule 3 - HISTONE DEACETYLASE COMPLEX SUBUNIT SAP18
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET SERIES
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Fragment: RESIDUES 14-143
    Organism Common: HUMAN
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: SAP18,18 KDA SIN3-ASSOCIATED POLYPEPTIDE, SIN3-ASSOCIATED POLYPEPTIDE P18

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4A8X)

(-) Sites  (0, 0)

(no "Site" information available for 4A8X)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4A8X)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr B:667 -Pro B:668

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4A8X)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.RNPS1_HUMAN161-240  1A:161-240

(-) Exons   (0, 0)

(no "Exon" information available for 4A8X)

(-) Sequences/Alignments

Asymmetric/Biological 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:88
 aligned with RNPS1_HUMAN | Q15287 from UniProtKB/Swiss-Prot  Length:305

    Alignment length:88
                                   166       176       186       196       206       216       226       236        
          RNPS1_HUMAN   157 SPKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVLAPWPR 244
               SCOP domains d4a8xa_ A: automated matches                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee......hhhhhhhhhhh...eeeee..ee..eeeee..eeeeee.hhhhhhhhhhhhh..ee..ee.eeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----RRM  PDB: A:161-240 UniProt: 161-240                                            ---- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 4a8x A 157 SMKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVLAPWPR 244
                                   166       176       186       196       206       216       226       236        


Chain B from PDB  Type:PROTEIN  Length:27
 aligned with Q9VJ12_DROME | Q9VJ12 from UniProtKB/TrEMBL  Length:739

    Alignment length:27
                                   665       675       
         Q9VJ12_DROME   656 LLDDLFRKTKGTPCIYWLPLTPEAIAE 682
               SCOP domains --------------------------- SCOP domains
               CATH domains --------------------------- CATH domains
               Pfam domains --------------------------- Pfam domains
         Sec.struct. author hhhhhhee.......eee..hhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------- SAPs(SNPs)
                    PROSITE --------------------------- PROSITE
                 Transcript --------------------------- Transcript
                 4a8x B 656 LLDDLFRKTKGTPCIYWLPLTPEAIAE 682
                                   665       675       


Chain C from PDB  Type:PROTEIN  Length:125
 aligned with SAP18_MOUSE | O55128 from UniProtKB/Swiss-Prot  Length:153

    Alignment length:125
                                    25        35        45        55        65        75        85        95       105       115       125       135     
          SAP18_MOUSE    16 PEKPIDREKTCPLLLRVFTTNNGRHHRMDEFSRGNVPSSELQIYTWMDATLKELTSLVKEVYPEARKKGTHFNFAIVFMDLKRPGYRVKEIGSTMSGRKGTDDSMTLQSQKFQIGDYLDIAITPP 140
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeeee......hhhhhhhhh.....eeeee....hhhhhhhhhhhhhhhhhh...eeeeeeeeee....eeeeeeeeeee...........hhhhh.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a8x C  16 PEKPIDREKTCPLLLRVFTTNNGRHHRMDEFSRGNVPSSELQIYTWMDATLKELTSLVKEVYPEARKKGTHFNFAIVFMDLKRPGYRVKEIGSTMSGRKGTDDSMTLQSQKFQIGDYLDIAITPP 140
                                    25        35        45        55        65        75        85        95       105       115       125       135
   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)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4A8X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4A8X)

(-) Gene Ontology  (34, 53)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RNPS1_HUMAN | Q15287)
molecular function
    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: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:0006405    RNA export from nucleus    The directed movement of RNA from the nucleus to the cytoplasm.
    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:0031124    mRNA 3'-end processing    Any process involved in forming the mature 3' end of an mRNA molecule.
    GO:0006406    mRNA export from nucleus    The directed movement of mRNA from the nucleus to the cytoplasm.
    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: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:0000184    nuclear-transcribed mRNA catabolic process, nonsense-mediated decay    The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    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:0006369    termination of RNA polymerase II transcription    The process in which the synthesis of an RNA molecule by RNA polymerase II using a DNA template is completed.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0061574    ASAP complex    A protein complex involved in regulation of mRNA processing and apoptosis. It binds to RNA in a sequence-independent manner and is recruited to the EJC prior to or during the splicing process. In humans the core proteins are RNPS1, SAP18 and ACIN1.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0035145    exon-exon junction complex    A multi-subunit complex deposited by the spliceosome upstream of messenger RNA exon-exon junctions. The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay.
    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.

Chain B   (Q9VJ12_DROME | Q9VJ12)
molecular function
    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: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: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:0000335    negative regulation of transposition, DNA-mediated    Any process that stops, prevents, or reduces the frequency, rate or extent of DNA transposition.
    GO:0006622    protein targeting to lysosome    The process of directing proteins towards the lysosome using signals contained within the protein.
    GO:0010506    regulation of autophagy    Any process that modulates the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
cellular component
    GO:0071013    catalytic step 2 spliceosome    A spliceosomal complex that contains three snRNPs, including U5, bound to a splicing intermediate in which the first catalytic cleavage of the 5' splice site has occurred. The precise subunit composition differs significantly from that of the catalytic step 1, or activated, spliceosome, and includes many proteins in addition to those found in the associated snRNPs.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0071011    precatalytic spliceosome    A spliceosomal complex that is formed by the recruitment of a preassembled U5-containing tri-snRNP to the prespliceosome. Although all 5 snRNPs are present, the precatalytic spliceosome is catalytically inactive. The precatalytic spliceosome includes many proteins in addition to those found in the associated snRNPs.

Chain C   (SAP18_MOUSE | O55128)
molecular function
    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:0000183    chromatin silencing at rDNA    Repression of transcription of ribosomal DNA by altering the structure of chromatin.
    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: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:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    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: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:0061574    ASAP complex    A protein complex involved in regulation of mRNA processing and apoptosis. It binds to RNA in a sequence-independent manner and is recruited to the EJC prior to or during the splicing process. In humans the core proteins are RNPS1, SAP18 and ACIN1.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0035145    exon-exon junction complex    A multi-subunit complex deposited by the spliceosome upstream of messenger RNA exon-exon junctions. The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay.
    GO:0000118    histone deacetylase complex    A protein complex that possesses histone deacetylase activity.
    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.
    GO:0005667    transcription factor complex    A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

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  4a8x
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  RNPS1_HUMAN | Q15287
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  SAP18_MOUSE | O55128
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 Related Entries

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

UniProtKB/Swiss-Prot
        SAP18_MOUSE | O55128: 4a6q 4a90

(-) Related Entries Specified in the PDB File

4a6q CRYSTAL STRUCTURE OF MOUSE SAP18 RESIDUES 6-143
4a90 STRUCTURE OF MOUSE SAP18 RESIDUES 1-143