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(-) Description

Title :  SOLUTION STRUCTURE OF A HUMAN UBIQUITIN-LIKE DOMAIN IN SF3A1
 
Authors :  J. A. Lukin, S. Dhe-Paganon, V. Guido, A. Lemak, G. V. Avvakumov, S. Xue, E. M. Newman, F. Mackenzie, M. Sundstrom, A. Edwards, C. H. Arrowsmith Structural Genomics Consortium (Sgc)
Date :  02 May 05  (Deposition) - 10 May 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Ubiquitin, Splicing Factor, Structural Genomics, Structural Genomics Consortium, Sgc, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. A. Lukin, S. Dhe-Paganon, V. Guido, A. Lemak, G. V. Avvakumov, S. Xue, E. M. Newman, F. Mackenzie, M. Sundstrom, A. Edwards, C. H. Arrowsmith
Solution Structure Of A Human Ubiquitin-Like Domain In Sf3A1
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SPLICING FACTOR 3 SUBUNIT 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET11
    Expression System StrainB21 (DE3) GOLD MAGIC
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUBIQUITIN-LIKE DOMAIN
    GeneSF3A1, SAP114
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSPLICEOSOME ASSOCIATED PROTEIN 114, SAP 114, SF3A120, SF3A1

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1ZKH)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.SF3A1_HUMAN707-790  1A:4-86

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002157931aENSE00001817075chr22:30752936-30752719218SF3A1_HUMAN1-21210--
1.2aENST000002157932aENSE00001332390chr22:30749061-30748940122SF3A1_HUMAN22-62410--
1.3bENST000002157933bENSE00000652198chr22:30742508-30742301208SF3A1_HUMAN62-131700--
1.4aENST000002157934aENSE00000652197chr22:30741179-30740922258SF3A1_HUMAN132-217860--
1.5aENST000002157935aENSE00001796702chr22:30738868-3073879475SF3A1_HUMAN218-242250--
1.6bENST000002157936bENSE00001361929chr22:30738339-30738189151SF3A1_HUMAN243-293510--
1.7aENST000002157937aENSE00000652194chr22:30737874-30737681194SF3A1_HUMAN293-357650--
1.8aENST000002157938aENSE00000652193chr22:30736801-30736684118SF3A1_HUMAN358-397400--
1.8eENST000002157938eENSE00001332338chr22:30736370-30736185186SF3A1_HUMAN397-459630--
1.9aENST000002157939aENSE00000652191chr22:30735240-30735119122SF3A1_HUMAN459-499410--
1.9eENST000002157939eENSE00001701251chr22:30735023-30734778246SF3A1_HUMAN500-581820--
1.10cENST0000021579310cENSE00001332326chr22:30733886-30733679208SF3A1_HUMAN582-651700--
1.11ENST0000021579311ENSE00000652188chr22:30733169-30733015155SF3A1_HUMAN651-702520--
1.12ENST0000021579312ENSE00000652187chr22:30731742-30731641102SF3A1_HUMAN703-736341A:1-3333
1.13ENST0000021579313ENSE00001332335chr22:30731527-3073145672SF3A1_HUMAN737-760241A:34-5724
1.14aENST0000021579314aENSE00001701490chr22:30730684-307296101075SF3A1_HUMAN761-793331A:58-8629

(-) 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:86
 aligned with SF3A1_HUMAN | Q15459 from UniProtKB/Swiss-Prot  Length:793

    Alignment length:86
                                   713       723       733       743       753       763       773       783      
          SF3A1_HUMAN   704 PVSIKVQVPNMQDKTEWKLNGQVLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMANGAVIHLALKERG 789
               SCOP domains d1zkha1 A:1-86 Splicing factor 3 subunit 1, C-terminal domain                          SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------ubiquitin-1zkhA01 A:14-85                                               - Pfam domains
         Sec.struct. author .eeeeee...............eeeeee....hhhhhhhhhhhhh......eeeee..eee....hhhhhh....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---UBIQUITIN_2  PDB: A:4-86 UniProt: 707-790                                           PROSITE
               Transcript 1 Exon 1.12  PDB: A:1-33           Exon 1.13  PDB: A:34-57 Exon 1.14a  PDB: A:58-86      Transcript 1
                 1zkh A   1 PVSIKVQVPNMQDKTEWKLNGQVLVFTLPLTDQVSVIKVKIHEATGMPAGKQKLQYEGIFIKDSNSLAYYNMANGAVIHLALKERG  86
                                    10        20        30        40        50        60        70        80      

   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  (1, 1)

NMR Structure

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1ZKH)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: Ubiquitin (279)

(-) Gene Ontology  (15, 15)

NMR Structure(hide GO term definitions)
Chain A   (SF3A1_HUMAN | Q15459)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    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:0000389    mRNA 3'-splice site recognition    Recognition of the intron 3'-splice site by components of the assembling U2- or U12-type spliceosome.
    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: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:0005686    U2 snRNP    A ribonucleoprotein complex that contains small nuclear RNA U2.
    GO:0071004    U2-type prespliceosome    A spliceosomal complex that is formed by association of the 5' splice site with the U1 snRNP, while the branch point sequence is recognized by the U2 snRNP. The prespliceosome includes many proteins in addition to those found in the U1 and U2 snRNPs. Commitment to a given pair of 5' and 3' splice sites occurs at the time of prespliceosome formation.
    GO:0005684    U2-type spliceosomal complex    Any spliceosomal complex that forms during the splicing of a messenger RNA primary transcript to excise an intron that has canonical consensus sequences near the 5' and 3' ends.
    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: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
        SF3A1_HUMAN | Q154592dt6 2dt7

(-) Related Entries Specified in the PDB File

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