Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
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 SURP DOMAIN IN SFRS14 PROTEI
 
Authors :  F. He, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  14 May 05  (Deposition) - 14 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Nmr, Surp Domain, Sfrs14 Protein, 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 Surp Domain In Sfrs14 Protei
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE SPLICING FACTOR, ARGININE/SERINE-RICH 14
    Chains: A
    Engineered: YES
    Expression System Plasmid: P041101-21
    Expression System Vector Type: PLASMID
    Fragment: SURP DOMAIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CELL FREE PROTEIN SYNTHESIS
    Synonym: SFRS14 PROTEIN, ARGININE/SERINE- RICH SPLICING FACTOR 14

 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 1X4P)

(-) Sites  (0, 0)

(no "Site" information available for 1X4P)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X4P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1X4P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X4P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1X4P)

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003370181ENSE00001511544chr19:19144380-19144246135SUGP2_HUMAN-00--
1.2bENST000003370182bENSE00001416917chr19:19141891-19141760132SUGP2_HUMAN1-41410--
1.3aENST000003370183aENSE00001122603chr19:19137035-191354281608SUGP2_HUMAN41-5775371A:1-7 (gaps)51
1.4ENST000003370184ENSE00000866130chr19:19130038-19129918121SUGP2_HUMAN577-617411A:8-3831
1.5ENST000003370185ENSE00000690765chr19:19121151-19120664488SUGP2_HUMAN617-7801641A:38-66 (gaps)139
1.6ENST000003370186ENSE00000690759chr19:19119237-19119126112SUGP2_HUMAN780-817380--
1.7bENST000003370187bENSE00001350867chr19:19115455-19114977479SUGP2_HUMAN817-9771610--
1.8ENST000003370188ENSE00000690750chr19:19112483-1911242262SUGP2_HUMAN977-997210--
1.9aENST000003370189aENSE00001221443chr19:19106089-19105953137SUGP2_HUMAN998-1043460--
1.9dENST000003370189dENSE00002186302chr19:19105295-19105175121SUGP2_HUMAN1043-1082400--
1.11bENST0000033701811bENSE00001560695chr19:19101958-19101697262SUGP2_HUMAN-00--

(-) 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:66
 aligned with SUGP2_HUMAN | Q8IX01 from UniProtKB/Swiss-Prot  Length:1082

    Alignment length:232
                                   533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753  
          SUGP2_HUMAN   524 GREYIDHLKAWLVSSGCPLQVKKAEPEPMREEEKMIPPTKPEIQAKAPSSLSDAVPQRADHRVVGTIDQLVKRVIEGSLSPKERTLLKEDPAYWFLSDENSLEYKYYKLKLAEMQRMSENLRGADQKPTSADCAVRAMLYSRAVRNLKKKLLPWQRRGLLRAQGLRGWKARRATTGTQTLLSSGTRLKHHGRQAPGLSQAKPSLPDRNDAAKDCPPDPVGPSPQDPSLEASG 755
               SCOP domains ---------------------------------------------------------------d1x4pa1 A:8-60                                       -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------Surp-1x4pA01 A:8-59                                 --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .------------...--------------------------------...------------.hhhhhhhhhhhh....hhhhhhhhh.....hhh.....hhhhhhhhhhhhhh.------------------------------------------------------------------------------------------------------...--------.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3a  PDB: A:1-7 (gaps) UniProt: 41-577          ---------------------------------------Exon 1.5  PDB: A:38-66 (gaps) UniProt: 617-780 [INCOMPLETE]                                                                                 Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------Exon 1.4  PDB: A:8-38 UniProt: 577-617   ------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 1x4p A   1 G------------SSG--------------------------------SSG------------VGTIDQLVKRVIEGSLSPKERTLLKEDPAYWFLSDENSLEYKYYKLKLAEMQRS------------------------------------------------------------------------------------------------------GPS--------SG  66
                            |        -   | |   -         -         -        |6|        -   |    14        24        34        44        54      |  -         -         -         -         -         -         -         -         -         -        62 |       -| 
                            |            2 4                                5 7            8                                                   61                                                                                                     62 |       65 
                            1                                                                                                                                                                                                                           64
   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, 1)

NMR Structure
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1X4P)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: Surp] (3)

(-) Gene Ontology  (7, 7)

NMR Structure(hide GO term definitions)
Chain A   (SUGP2_HUMAN | Q8IX01)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
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: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.
cellular component
    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.

 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 1x4p)
 
  Sites
(no "Sites" information available for 1x4p)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1x4p)
 

(-) 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
  1x4p
    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
  SUGP2_HUMAN | Q8IX01
    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
  SUGP2_HUMAN | Q8IX01
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1X4P)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1X4P)