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(-) Description

Title :  CRYSTAL STRUCTURE OF PQBP1 BOUND TO SPLICEOSOMAL U5-15KD
 
Authors :  M. Mizuguchi, T. Obita, T. Serita, R. Kojima, Y. Nabeshima, H. Okazawa
Date :  05 Nov 13  (Deposition) - 30 Apr 14  (Release) - 14 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,C
Biol. Unit 1:  C  (1x)
Biol. Unit 2:  A  (1x)
Keywords :  Cell Cycle, U5-52Kd (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Mizuguchi, T. Obita, T. Serita, R. Kojima, Y. Nabeshima, H. Okazawa
Mutations In The Pqbp1 Gene Prevent Its Interaction With The Spliceosomal Protein U5-15Kd.
Nat. Commun. V. 5 3822 2014
PubMed-ID: 24781215  |  Reference-DOI: 10.1038/NCOMMS4822

(-) Compounds

Molecule 1 - THIOREDOXIN-LIKE PROTEIN 4A, POLYGLUTAMINE-BINDING PROTEIN
    ChainsA, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantC41
    Expression System VectorPOPTH
    Expression System Vector TypePLASMID
    FragmentRESIDUES 4-137,223-265
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDIM1 PROTEIN HOMOLOG, SPLICEOSOMAL U5 SNRNP-SPECIFIC 15 KDA PROTEIN, THIOREDOXIN-LIKE U5 SNRNP PROTEIN U5-15KD, PQBP-1,38 KDA NUCLEAR PROTEIN CONTAINING A WW DOMAIN, NPW38, POLYGLUTAMINE TRACT-BINDING PROTEIN 1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AC
Biological Unit 1 (1x) C
Biological Unit 2 (1x)A 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 4CDO)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4CDO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4CDO)

(-) Exons   (3, 6)

Asymmetric Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002696011aENSE00001274525chr18:77748532-77748240293TXN4A_HUMAN1-51512A:4-51
C:4-51
48
48
1.2ENST000002696012ENSE00000950773chr18:77737701-77737598104TXN4A_HUMAN52-86352A:52-86
C:52-86
35
35
1.4ENST000002696014ENSE00000996738chr18:77733856-77732869988TXN4A_HUMAN86-142572A:86-247 (gaps)
C:86-254 (gaps)
57
63

(-) 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:150
 aligned with TXN4A_HUMAN | P83876 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:151
                                                                                                                                                                    142            
                                    13        23        33        43        53        63        73        83        93       103       113       123       133        |-         - 
          TXN4A_HUMAN     4 MLPHLHNGWQVDQAILSEEDRVVVIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYLVDITEVPDFNKMYELYDPCTVMFFFRNKHIMIDLGTGNNNKINWAMEDKQEMVDIIETVYRGARKGRGLVVSPKDYSTKYRY------------   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.hhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhh......eeeeeee.................eeeeee..ee.eee..............hhhhhhhhhhhhhhhhhh...eee......-...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:4-51 UniProt: 1-51            Exon 1.2  PDB: A:52-86             -------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------Exon 1.4  PDB: A:86-247 (gaps) UniProt: 86-142           ------------ Transcript 1 (2)
                 4cdo A   4 MLPHLHNGWQVDQAILSEEDRVVVIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYLVDITEVPDFNKMYELYDPCTVMFFFRNKHIMIDLGTGNNNKINWAMEDKQEMVDIIETVYRGARKGRGLVVSPKDYS-PYPSPGAVLRANAEAS 259
                                    13        23        33        43        53        63        73        83        93       103       113       123       133   | | 248       258 
                                                                                                                                                               137 |               
                                                                                                                                                                 244               

Chain C from PDB  Type:PROTEIN  Length:149
 aligned with TXN4A_HUMAN | P83876 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:149
                                                                                                                                                              136   137  142     
                                    13        23        33        43        53        63        73        83        93       103       113       123       133  |    138   |     
          TXN4A_HUMAN     4 MLPHLHNGWQVDQAILSEEDRVVVIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYLVDITEVPDFNKMYELYDPCTVMFFFRNKHIMIDLGTGNNNKINWAMEDKQEMVDIIETVYRGARKGRGLVVSPKDY-----STKYRY-----   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.hhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhh......eeeeeee.................eeeeee..ee.eee..............hhhhhhhhhhhhhhhhhh...eee........hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: C:4-51 UniProt: 1-51            Exon 1.2  PDB: C:52-86             ------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------Exon 1.4  PDB: C:86-254 (gaps) UniProt: 86-142                ----- Transcript 1 (2)
                 4cdo C   4 MLPHLHNGWQVDQAILSEEDRVVVIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYLVDITEVPDFNKMYELYDPCTVMFFFRNKHIMIDLGTGNNNKINWAMEDKQEMVDIIETVYRGARKGRGLVVSPKDYPYPSPGAVLRANAEAS 259
                                    13        23        33        43        53        63        73        83        93       103       113       123       133  ||   250         
                                                                                                                                                              136|               
                                                                                                                                                               244               

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 4CDO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (30, 35)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (TXN4A_HUMAN | P83876)
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:0000375    RNA splicing, via transesterification reactions    Splicing of RNA via a series of two transesterification reactions.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    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:0000245    spliceosomal complex assembly    The aggregation, arrangement and bonding together of a spliceosomal complex, a ribonucleoprotein apparatus that catalyzes nuclear mRNA splicing via transesterification reactions.
cellular component
    GO:0046540    U4/U6 x U5 tri-snRNP complex    A ribonucleoprotein complex formed by the association of the U4/U6 and U5 small nuclear ribonucleoproteins.
    GO:0005682    U5 snRNP    A ribonucleoprotein complex that contains small nuclear RNA U5.
    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: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
        PQBP1_HUMAN | O608284bwq 4bws
        TXN4A_HUMAN | P838761pqn 1qgv 1syx 3jcr 4bwq 4bws

(-) Related Entries Specified in the PDB File

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