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 RRM OF SRP20 BOUND TO THE RNA CAUC
 
Authors :  Y. F. Hargous, F. H. Allain
Date :  17 Aug 06  (Deposition) - 12 Dec 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (28x)
Keywords :  Protein-Rna Complex Rrm Alpha-Beta Sandwich Beta1-Alpha1- Beta2-Beta3-Alpha2-Beta4, Rna Binding Protein/Chimera/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Hargous, G. M. Hautbergue, A. M. Tintaru, L. Skrisovska, A. P. Golovanov, J. Stevenin, L. Y. Lian, S. A. Wilson, F. H. Allain
Molecular Basis Of Rna Recognition And Tap Binding By The Sr Proteins Srp20 And 9G8.
Embo J. V. 25 5126 2006
PubMed-ID: 17036044  |  Reference-DOI: 10.1038/SJ.EMBOJ.7601385
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FUSION PROTEIN CONSISTS OF IMMUNOGLOBIN G- BINDING PROTEIN G AND SPLICING FACTOR, ARGININE/SERINE- RICH 3
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)CODON+ RIL
    Expression System Taxid562
    Expression System VectorPET-28
    Expression System Vector TypePLASMID
    FragmentRRM DOMAIN
    GeneSPG AND SFRS3
    Organism Common, HUMAN
    Organism ScientificSTREPTOCOCCUS SP. 'GROUP G', HOMO SAPIENS
    Organism Taxid1320,9606
    Strain,
    SynonymPRE-MRNA-SPLICING FACTOR SRP20
 
Molecule 2 - (5'-R(*CP*AP*UP*C)-3')
    ChainsB
    EngineeredYES
    Other DetailsCORE SEQUENCE OF EXONIC SPLICING ENHANCERS RECOGNISED BY SRP20
    SyntheticYES

 Structural Features

(-) Chains, Units

  
NMR Structure (28x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2I2Y)

(-) Sites  (0, 0)

(no "Site" information available for 2I2Y)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2I2Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2I2Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2I2Y)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.SRSF3_HUMAN10-83  1A:74-147
2GRAM_POS_ANCHORINGPS50847 Gram-positive cocci surface proteins LPxTG motif profile.SPG2_STRSG559-593  1A:134-150

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003737151bENSE00001848923chr6:36562145-36562258114SRSF3_HUMAN-00--
1.2ENST000003737152ENSE00002148108chr6:36564538-36564745208SRSF3_HUMAN1-69691A:65-13369
1.3ENST000003737153ENSE00002189851chr6:36566626-36566760135SRSF3_HUMAN69-114461A:133-15018
1.5ENST000003737155ENSE00002186182chr6:36568929-3656896739SRSF3_HUMAN114-127140--
1.6bENST000003737156bENSE00000849740chr6:36569485-3656957187SRSF3_HUMAN127-156300--
1.7bENST000003737157bENSE00001027890chr6:36569739-365712091471SRSF3_HUMAN156-16490--

(-) 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:150
 aligned with SPG2_STRSG | P19909 from UniProtKB/Swiss-Prot  Length:593

    Alignment length:289
                                   311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581         
           SPG2_STRSG   302 DTYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEKPEVIDASELTPAVTTYKLVINGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEKPEVIDASELTPAVTTYKLVINGKTLKGETTTKAVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVTEMVTEVPGDAPTEPEKPEASIPLVPLTPATPIAKDDAKKDDTKKEDAKKPEAKKEDAKKAETLPTTGEGSNPFFTAAALAVMAGAGALAVASKR 590
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......eeeeee..hhhhhh.hhhhhhhhhh...eeeee....eeeee..--------------------------.................eeeee......--------------------.hhhh------------------------------hhhhhhhh---.eeeeee....-------------..eeeeee.hh----------------hhhh--hhhhhhh..--------------------------.......ee---ee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GRAM_POS_ANCHORING               PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i2y A   1 MQYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEG--------------------------SHHHHHHMHRDSCPLDCKVYVGNLGNNG--------------------NKTEL------------------------------ERAFGYYG---PLRSVWVARNP-------------PGFAFVEFEDP----------------RDAA--DAVRELDGR--------------------------TLCGCRVRV---ELSNGEKR 150
                                    10        20        30        40        50      |  -         -         -   |    64        74        84|        -         - |   |   -         -         -      | 94   |   101       | -         - |     118 |       -       122 |  |  130  |      -         -       134       | - |       
                                                                                   57                         58                         85                   86  90                             91     98  99       109           110       120              121  |  |     133                        134     142 143       
                                                                                                                                                                                                                                                                 124  |                                                      
                                                                                                                                                                                                                                                                    125                                                      

Chain A from PDB  Type:PROTEIN  Length:150
 aligned with SRSF3_HUMAN | P84103 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:150
                                                                                            1                                                                                     
                                     -         -         -         -         -         -    |    6        16        26        36        46        56        66        76        86
          SRSF3_HUMAN     - ----------------------------------------------------------------MHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEKR  86
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee......eeeeee..hhhhhh.hhhhhhhhhh...eeeee....eeeee...................eeeee.......hhhhhhhhhhhh.eeeeee......eeeeee.hhhhhhhhhhhhh.........eeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------RRM  PDB: A:74-147 UniProt: 10-83                                         --- PROSITE
           Transcript 1 (1) ----------------------------------------------------------------Exon 1.2  PDB: A:65-133 UniProt: 1-69                                ----------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------------Exon 1.3           Transcript 1 (2)
                 2i2y A   1 MQYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEKR 150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain B from PDB  Type:RNA  Length:4
                                    
                 2i2y B 151 CAUC 154

   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 2I2Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2I2Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2I2Y)

(-) Gene Ontology  (25, 27)

NMR Structure(hide GO term definitions)
Chain A   (SPG2_STRSG | P19909)
molecular function
    GO:0019864    IgG binding    Interacting selectively and non-covalently with an immunoglobulin of an IgG isotype.
biological process
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain A   (SRSF3_HUMAN | P84103)
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.
    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:0043274    phospholipase binding    Interacting selectively and non-covalently with any phospholipase, enzymes that catalyze of the hydrolysis of a glycerophospholipid.
    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:1990825    sequence-specific mRNA binding    Interacting selectively and non-covalently with messenger RNA (mRNA) of a specific nucleotide composition or a specific sequence motif.
biological process
    GO:0006405    RNA export from nucleus    The directed movement of RNA from the nucleus to the cytoplasm.
    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:0031124    mRNA 3'-end processing    Any process involved in forming the mature 3' end of an mRNA molecule.
    GO:0006406    mRNA export from nucleus    The directed movement of mRNA from the nucleus to the cytoplasm.
    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:0051028    mRNA transport    The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0048024    regulation of mRNA splicing, via spliceosome    Any process that modulates the frequency, rate or extent of mRNA splicing via a spliceosomal mechanism.
    GO:0006369    termination of RNA polymerase II transcription    The process in which the synthesis of an RNA molecule by RNA polymerase II using a DNA template is completed.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016607    nuclear speck    A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
    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 2i2y)
 
  Sites
(no "Sites" information available for 2i2y)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2i2y)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2i2y
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SPG2_STRSG | P19909
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  SRSF3_HUMAN | P84103
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  SPG2_STRSG | P19909
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  SRSF3_HUMAN | P84103
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SPG2_STRSG | P199091fcc 1fcl 1fd6 1gb4 1gjs 1gjt 1ibx 1p7e 1p7f 1qkz 1uwx 1zxh 2gi9 2i38 2igg 2jsv 2ju6 2khu 2khw 2kn4 2kq4 2kwd 2lum 2n9k 2n9l 2oed 2on8 2onq 2plp 2qmt 3fil 3ui3 3v3x 4oza 4ozb 4ozc 4wh4 5bmg 5bmh 5bmi 5hfy 5hg2 5hi1
        SRSF3_HUMAN | P841032i38

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2I2Y)