Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - manually
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - manually
NMR Structure - manually  (Jmol Viewer)
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF THE SURP2 DOMAIN IN SPLICING FACTOR, ARGININE/SERINE-RICH 8
 
Authors :  F. He, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  25 Dec 06  (Deposition) - 26 Jun 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Nmr, Surp Domain, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. He, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama
Solution Structure Of The Surp2 Domain In Splicing Factor, Arginine/Serine-Rich 8
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SPLICING FACTOR, ARGININE/SERINE-RICH 8
    Chains: A
    Engineered: YES
    Expression System Plasmid: P060320-08
    Expression System Vector Type: PLASMID
    Fragment: SURP DOMAIN
    Gene: SFRS8, SWAP
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CELL FREE PROTEIN SYNTHESIS
    Synonym: SFRS8 PROTEIN

 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 2E5Z)

(-) Sites  (0, 0)

(no "Site" information available for 2E5Z)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2E5Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2E5Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_057248G512SSFSWA_HUMANPolymorphism34541796AG80S
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SURPPS50128 SURP motif repeat profile.SFSWA_HUMAN211-253
459-499		  1-
A:27-67

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002616741ENSE00001192361chr12:132195635-132195992358SFSWA_HUMAN1-73730--
1.2ENST000002616742ENSE00000757545chr12:132198616-132198785170SFSWA_HUMAN73-130580--
1.3ENST000002616743ENSE00000757546chr12:132199367-132199498132SFSWA_HUMAN130-174450--
1.4ENST000002616744ENSE00000757547chr12:132203999-13220408486SFSWA_HUMAN174-202290--
1.5ENST000002616745ENSE00000757548chr12:132209950-132210175226SFSWA_HUMAN203-278760--
1.6ENST000002616746ENSE00000757549chr12:132211485-132211597113SFSWA_HUMAN278-315380--
1.7ENST000002616747ENSE00000757550chr12:132212838-132212973136SFSWA_HUMAN316-361460--
1.8ENST000002616748ENSE00001192354chr12:132237668-132237908241SFSWA_HUMAN361-441811A:1-9 (gaps)13
1.9ENST000002616749ENSE00000757553chr12:132238913-132239044132SFSWA_HUMAN441-485451A:9-5345
1.10ENST0000026167410ENSE00000757554chr12:132239931-13224002494SFSWA_HUMAN485-516321A:53-8432
1.11ENST0000026167411ENSE00000757555chr12:132241018-132241189172SFSWA_HUMAN517-574581A:85-906
1.12ENST0000026167412ENSE00000757556chr12:132249001-132249231231SFSWA_HUMAN574-651780--
1.13ENST0000026167413ENSE00001192340chr12:132250663-132250853191SFSWA_HUMAN651-714640--
1.14ENST0000026167414ENSE00001222569chr12:132262610-132262875266SFSWA_HUMAN715-803890--
1.15ENST0000026167415ENSE00001297565chr12:132271008-132271133126SFSWA_HUMAN803-845430--
1.16ENST0000026167416ENSE00001318201chr12:132281723-132281905183SFSWA_HUMAN845-906620--
1.17ENST0000026167417ENSE00001290833chr12:132283582-13228365473SFSWA_HUMAN906-930250--
1.18ENST0000026167418ENSE00001305898chr12:132283968-132284282315SFSWA_HUMAN931-951210--

(-) 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:90
 aligned with Q8IV81_HUMAN | Q8IV81 from UniProtKB/TrEMBL  Length:547

    Alignment length:94
                                   375       385       395       405       415       425       435       445       455    
         Q8IV81_HUMAN   366 TSSGATSTTTTTSALAPVAAIIPPPPDVQPVIDKLAEYVARNGLKFETSVRAKNDQRFEFLQPWHQYNAYYEFKKQFFLQKEGGDSMQAVSAPE 459
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......----.................hhhhhhhhhhhhh..hhhhhhhhhh..hhh........hhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------S---------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 2e5z A   1 GSSGSSG----TSALAPVAAIIPPPPDVQPVIDKLAEYVARNGLKFETSVRAKNDQRFEFLQPWHQYNAYYEFKKQFFLQKEGGDSMQAVSAPE  90
                                  |  - |      16        26        36        46        56        66        76        86    
                                  7    8                                                                                  


Chain A from PDB  Type:PROTEIN  Length:90
 aligned with SFSWA_HUMAN | Q12872 from UniProtKB/Swiss-Prot  Length:951

    Alignment length:94
                                   438       448       458       468       478       488       498       508       518    
          SFSWA_HUMAN   429 TSSGATSTTTTTSALAPVAAIIPPPPDVQPVIDKLAEYVARNGLKFETSVRAKNDQRFEFLQPWHQYNAYYEFKKQFFLQKEGGDSMQAVSAPE 522
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......----.................hhhhhhhhhhhhh..hhhhhhhhhh..hhh........hhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------S---------- SAPs(SNPs)
                    PROSITE ------------------------------SURP  PDB: A:27-67 UniProt: 459-499      ----------------------- PROSITE
           Transcript 1 (1) Exon 1.8     -------------------------------------------Exon 1.10  PDB: A:53-84         1.11   Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.9  PDB: A:9-53 UniProt: 441-485       ------------------------------------- Transcript 1 (2)
                 2e5z A   1 GSSGSSG----TSALAPVAAIIPPPPDVQPVIDKLAEYVARNGLKFETSVRAKNDQRFEFLQPWHQYNAYYEFKKQFFLQKEGGDSMQAVSAPE  90
                                  |  - |      16        26        36        46        56        66        76        86    
                                  7    8
   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 2E5Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2E5Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2E5Z)

(-) Gene Ontology  (11, 13)

NMR Structure(hide GO term definitions)
Chain A   (SFSWA_HUMAN | Q12872)
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:0000380    alternative mRNA splicing, via spliceosome    The process of generating multiple mRNA molecules from a given set of exons by differential use of exons from the primary transcript(s) to form multiple mature mRNAs that vary in their exon composition.
    GO:0000395    mRNA 5'-splice site recognition    Recognition of the intron 5'-splice site by components of the assembling 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: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: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: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 A   (Q8IV81_HUMAN | Q8IV81)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
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.

 Visualization

(-) Interactive Views

NMR Structure
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2e5z)
 
  Sites
(no "Sites" information available for 2e5z)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2e5z)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - all models PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2e5z
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q8IV81_HUMAN | Q8IV81
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  SFSWA_HUMAN | Q12872
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q8IV81_HUMAN | Q8IV81
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  SFSWA_HUMAN | Q12872
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        Q8IV81_HUMAN | Q8IV81: 2e60
        SFSWA_HUMAN | Q12872: 2e60

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2E5Z)