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(-) Description

Title :  STRUCTURE OF URNDESIGN, A COMPLETE COMPUTATIONAL REDESIGN OF HUMAN U1A PROTEIN
 
Authors :  G. Varani, N. Dobson, G. Dantas, D. Baker
Date :  24 Jun 05  (Deposition) - 06 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Computationally Designed Protein, Rrm, U1A, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Dobson, G. Dantas, D. Baker, G. Varani
High-Resolution Structural Validation Of The Computational Redesign Of Human U1A Protein
Structure V. 14 847 2006
PubMed-ID: 16698546  |  Reference-DOI: 10.1016/J.STR.2006.02.011
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET 29(B)
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRNA BINDING DOMAIN, RESIDUES 2-97
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCOMPUTATIONALLY REDESIGNED VARIANT
    SynonymU1 SNRNP PROTEIN A, U1A PROTEIN, U1-A

 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 2A3J)

(-) Sites  (0, 0)

(no "Site" information available for 2A3J)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2A3J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2A3J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2A3J)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.SNRPA_HUMAN10-89
208-282
  1A:34-109
-

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002435631ENSE00001052136chr19:41256779-41257386608SNRPA_HUMAN1-25251A:22-4524
1.2ENST000002435632ENSE00000707951chr19:41263237-41263409173SNRPA_HUMAN25-82581A:45-10258
1.3ENST000002435633ENSE00000707956chr19:41265336-41265515180SNRPA_HUMAN83-142601A:103-11715
1.4ENST000002435634ENSE00000707961chr19:41268806-41268979174SNRPA_HUMAN143-200580--
1.5ENST000002435635ENSE00000842333chr19:41269492-4126958089SNRPA_HUMAN201-230300--
1.6ENST000002435636ENSE00000842334chr19:41270913-41271290378SNRPA_HUMAN230-282530--

(-) 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:96
 aligned with SNRPA_HUMAN | P09012 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:96
                                    11        21        31        41        51        61        71        81        91      
          SNRPA_HUMAN     2 AVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKM  97
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeee......hhhhhhhhhhhhhhhhh.eeeeee.........eeeee.hhhhhhhhhhhh..........eeee....hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------RRM  PDB: A:34-109 UniProt: 10-89                                               -------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:22-45  ---------------------------------------------------------Exon 1.3        Transcript 1 (1)
           Transcript 1 (2) -----------------------Exon 1.2  PDB: A:45-102 UniProt: 25-82                    --------------- Transcript 1 (2)
                 2a3j A  22 TPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQSQVAED 117
                                    31        41        51        61        71        81        91       101       111      

   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  (0, 0)

(no "SCOP Domain" information available for 2A3J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2A3J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2A3J)

(-) Gene Ontology  (17, 17)

NMR Structure(hide GO term definitions)
Chain A   (SNRPA_HUMAN | P09012)
molecular function
    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: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).
    GO:0017069    snRNA binding    Interacting selectively and non-covalently with a small nuclear RNA (snRNA).
    GO:0035614    snRNA stem-loop binding    Interacting selectively and non-covalently with a stem-loop in a small nuclear RNA (snRNA). An RNA stem-loop is a secondary RNA structure consisting of a double-stranded RNA (dsRNA) stem and a terminal loop.
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: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.
cellular component
    GO:0005685    U1 snRNP    A ribonucleoprotein complex that contains small nuclear RNA U1.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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
        SNRPA_HUMAN | P090121aud 1drz 1dz5 1fht 1m5k 1m5o 1m5p 1m5v 1nu4 1oia 1sj3 1sj4 1sjf 1u6b 1urn 1vbx 1vby 1vbz 1vc0 1vc5 1vc6 1zzn 2nz4 2oih 2oj3 2u1a 3bo2 3bo3 3bo4 3cul 3cun 3egz 3g8s 3g8t 3g96 3g9c 3hhn 3iin 3irw 3iwn 3k0j 3l3c 3mum 3mur 3mut 3muv 3mxh 3p49 3pgw 3r1h 3r1l 3ucu 3ucz 3ud3 3ud4 3utr 4c4w 4pr6 4prf 4w90 4w92 4yb1 5ddo 5ddp 5ddq 5ddr 5fj4

(-) Related Entries Specified in the PDB File

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