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(-) Description

Title :  CRYSTAL STRUCTURE OF PRP8 CORE DOMAIN IV
 
Authors :  M. J. Schellenberg, D. B. Ritchie, A. M. Macmillan
Date :  25 Sep 08  (Deposition) - 07 Oct 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Prp8 Domain Iv, Beta Finger, Rnase H, Spliceosome, U5-220K, Disease Mutation, Mrna Processing, Mrna Splicing, Nucleus, Phosphoprotein, Retinitis Pigmentosa, Rna-Binding, Sensory Transduction, Vision, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. B. Ritchie, M. J. Schellenberg, E. M. Gesner, S. A. Raithatha, D. T. Stuart, A. M. Macmillan
Structural Elucidation Of A Prp8 Core Domain From The Heart Of The Spliceosome.
Nat. Struct. Mol. Biol. V. 15 1199 2008
PubMed-ID: 18836455  |  Reference-DOI: 10.1038/NSMB.1505

(-) Compounds

Molecule 1 - PRE-MRNA-PROCESSING-SPLICING FACTOR 8
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMALC2X
    Expression System StrainBL21
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 1769-1990
    GenePRPF8, PRPC8
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSPLICING FACTOR PRP8, PRP8 HOMOLOG, 220 KDA U5 SNRNP- SPECIFIC PROTEIN, P220

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3ENB)

(-) Sites  (0, 0)

(no "Site" information available for 3ENB)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ENB)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ENB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ENB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ENB)

(-) Exons   (0, 0)

(no "Exon" information available for 3ENB)

(-) Sequences/Alignments

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:219
 aligned with PRP8_HUMAN | Q6P2Q9 from UniProtKB/Swiss-Prot  Length:2335

    Alignment length:219
                                  1780      1790      1800      1810      1820      1830      1840      1850      1860      1870      1880      1890      1900      1910      1920      1930      1940      1950      1960      1970      1980         
          PRP8_HUMAN   1771 LFSNQIIWFVDDTNVYRVTIHKTFEGNLTTKPINGAIFIFNPRTGQLFLKIIHTSVWAGQKRLGQLAKWKTAEEVAALIRSLPVEEQPKQIIVTRKGMLDPLEVHLLDFPNIVIKGSELQLPFQACLKVEKFGDLILKATEPQMVLFNLYDDWLKTISSYTAFSRLILILRALHVNNDRAKVILKPDKTTITEPHHIWPTLTDEEWIKVEVQLKDLILA 1989
               SCOP domains d3enba1 A:1771-1989 Pre-mRNA-splicing factor 8, Prp8                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee.....eeeeee.....eeeeee.eeeeee.....eeeeeeehhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhhhhhh...eeeeee...hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3enb A 1771 LFSNQIIWFVDDTNVYRVTIHKTFEGNLTTKPINGAIFIFNPRTGQLFLKIIHTSVWAGQKRLGQLAKWKTAEEVAALIRSLPVEEQPKQIIVTRKGMLDPLEVHLLDFPNIVIKGSELQLPFQACLKVEKFGDLILKATEPQMVLFNLYDDWLKTISSYTAFSRLILILRALHVNNDRAKVILKPDKTTITEPHHIWPTLTDEEWIKVEVQLKDLILA 1989
                                  1780      1790      1800      1810      1820      1830      1840      1850      1860      1870      1880      1890      1900      1910      1920      1930      1940      1950      1960      1970      1980         

Chain B from PDB  Type:PROTEIN  Length:203
 aligned with PRP8_HUMAN | Q6P2Q9 from UniProtKB/Swiss-Prot  Length:2335

    Alignment length:215
                                  1783      1793      1803      1813      1823      1833      1843      1853      1863      1873      1883      1893      1903      1913      1923      1933      1943      1953      1963      1973      1983     
          PRP8_HUMAN   1774 NQIIWFVDDTNVYRVTIHKTFEGNLTTKPINGAIFIFNPRTGQLFLKIIHTSVWAGQKRLGQLAKWKTAEEVAALIRSLPVEEQPKQIIVTRKGMLDPLEVHLLDFPNIVIKGSELQLPFQACLKVEKFGDLILKATEPQMVLFNLYDDWLKTISSYTAFSRLILILRALHVNNDRAKVILKPDKTTITEPHHIWPTLTDEEWIKVEVQLKDLIL 1988
               SCOP domains d3enbb_ B: Pre-m            RNA-splicing factor 8, Prp8                                                                                                                                                                 SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.....------------...eeeeee.....eeeeeee...hhhhh......hhhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhh......eeee.....hhhhhhhhhhhhhhhhhh...eeeeee...hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3enb B 1774 NQIIWFVDDTNVYRVT------------PINGAIFIFNPRTGQLFLKIIHTSVWAGQKRLGQLAKWKTAEEVAALIRSLPVEEQPKQIIVTRKGMLDPLEVHLLDFPNIVIKGSELQLPFQACLKVEKFGDLILKATEPQMVLFNLYDDWLKTISSYTAFSRLILILRALHVNNDRAKVILKPDKTTITEPHHIWPTLTDEEWIKVEVQLKDLIL 1988
                                  1783     |   -      1803      1813      1823      1833      1843      1853      1863      1873      1883      1893      1903      1913      1923      1933      1943      1953      1963      1973      1983     
                                        1789         1802                                                                                                                                                                                          

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ENB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ENB)

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PRP8_HUMAN | Q6P2Q9)
molecular function
    GO:0070530    K63-linked polyubiquitin modification-dependent protein binding    Interacting selectively and non-covalently with a protein upon poly-ubiquitination formed by linkages between lysine residues at position 63 in the target protein.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0030619    U1 snRNA binding    Interacting selectively and non-covalently with the U1 small nuclear RNA (U1 snRNA).
    GO:0030620    U2 snRNA binding    Interacting selectively and non-covalently with the U2 small nuclear RNA (U2 snRNA).
    GO:0030623    U5 snRNA binding    Interacting selectively and non-covalently with the U5 small nuclear RNA (U5 snRNA).
    GO:0017070    U6 snRNA binding    Interacting selectively and non-covalently with the U6 small nuclear RNA (U6 snRNA).
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0097157    pre-mRNA intronic binding    Interacting selectively and non-covalently with an intronic sequence of a pre-messenger RNA (pre-mRNA).
    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:0000386    second spliceosomal transesterification activity    Catalysis of the second transesterification reaction of spliceosomal mRNA splicing. Ligation of the two exons occurs via a transesterification reaction where the free 3'-hydroxyl group of the 5' exon is the nucleophile attacking the 3' splice site. Non-expressed sequences are now detached from the exons. In cis splicing, the intron is in a lariat structure.
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:0071222    cellular response to lipopolysaccharide    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0071356    cellular response to tumor necrosis factor    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tumor necrosis factor stimulus.
    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:0000244    spliceosomal tri-snRNP complex assembly    The formation of a tri-snRNP complex containing U4 and U6 (or U4atac and U6atac) snRNAs and U5 snRNAs and associated proteins. This includes reannealing of U4 and U6 (or U4atac and U6atac) snRNAs released from previous rounds of splicing to reform the U4/U6 snRNP (or U4atac/U6atac snRNP) as well as the subsequent association of the U5 snRNP with the U4/U6 snRNP (or U4atac/U6atac snRNP) to form a tri-snRNP that is ready to reassemble into another spliceosome complex.
cellular component
    GO:0005682    U5 snRNP    A ribonucleoprotein complex that contains small nuclear RNA U5.
    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:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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:0030532    small nuclear ribonucleoprotein complex    A complex composed of RNA of the small nuclear RNA (snRNA) class and protein, found in the nucleus of a eukaryotic cell. These are typically named after the snRNA(s) they contain, e.g. U1 snRNP or U4/U6 snRNP. Many, but not all, of these complexes are involved in splicing of nuclear mRNAs.
    GO:0005681    spliceosomal complex    Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PRP8_HUMAN | Q6P2Q93e9l 3jcr 3lru 4jk7 4jk8 4jk9 4jka 4jkb 4jkc 4jkd 4jke 4jkf 4jkg 4jkh 4kit 5mqf

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