Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF PRP8:AAR2 COMPLEX
 
Authors :  W. P. Galej, C Oubridge, A. J. Newman, K Nagai
Date :  27 Nov 12  (Deposition) - 23 Jan 13  (Release) - 13 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Spliceosome, U5 Snrnp, Prp8, Reverse Transcriptase, Aar2, Endonuclease, Rnase H, Jab1/Mpn, Pre-Mrna Splicing, Splicing (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. P. Galej, C. Oubridge, A. J. Newman, K. Nagai
Crystal Structure Of Prp8 Reveals Active Site Cavity Of The Spliceosome.
Nature V. 493 638 2013
PubMed-ID: 23354046  |  Reference-DOI: 10.1038/NATURE11843

(-) Compounds

Molecule 1 - A1 CISTRON-SPLICING FACTOR AAR2
    Chains: A
    Engineered: YES
    Expression System: SACCHAROMYCES CEREVISIAE
    Expression System Plasmid: MODIFIED PRS424
    Expression System Strain: BCY123
    Expression System Taxid: 4932
    Expression System Vector Type: PLASMID
    Gene: AAR2, YBL074C, YBL06.06, YBL0611
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
 
Molecule 2 - PRE-MRNA-SPLICING FACTOR 8
    Chains: B
    Engineered: YES
    Expression System: SACCHAROMYCES CEREVISIAE
    Expression System Plasmid: MODIFIED PRS426
    Expression System Strain: BCY123
    Expression System Taxid: 4932
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 885-2413
    Gene: PRP8, DBF3, DNA39, RNA8, SLT21, USA2, YHR165C
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4I43)

(-) Sites  (0, 0)

(no "Site" information available for 4I43)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4I43)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys B:1014 -Pro B:1015
2Ile B:1488 -Pro B:1489

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4I43)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4I43)

(-) Exons   (0, 0)

(no "Exon" information available for 4I43)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   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:334
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.......eeeee..eeeee.......eee.......eeeeeee.......eeeeehhhhh.eeeeee....eeeeee..hhhhhhhh....ee.......hhhhhhhh..hhhhhhhhh.......eeee...eehhhhhhhhhhh......hhh.ee................hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh...................eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4i43 A    2 NTVPFTSAPIEVTIGIDQYSFNVKENQPFHGIKDIPIGHVHVIHFQHADNSSMRYGYWFDCRMGNFYIQYDPKDGLYKMMEERDGAKFENIRQMMVSYPKIDEDDTWYNLTEFVQMDKIRKIVRKDENQFSYVDSSMTTVQENELLKSSLEAKNEDDPAHSLNYTVINFKSREAIRPGHEMEDFLDKSYYLNTVMLQGIFKNSSNYFGELQFAFLNAMFFGNYGSSLQWHAMIELICSSATVPKHMLDKLDEILYYQIKTLPEQYSDILLNERVWNICLYSSFQKNSLHNTEKIMENKYPELLGKDNDDALIYGDDEDDEHNPTIVGGLYYQRP  355
                                    11        21        31        41        51        61        71        81        91||     107       117       127       137       147       157|      174       184       194       204       214       224       234       244       254       264       274       284       294       304       314      |325   ||  341       351    
                                                                                                                     92|                                                       157|                                                                                                                                                         321|   329|                   
                                                                                                                      99                                                        165                                                                                                                                                          323    336                   


Chain B from PDB  Type:PROTEIN  Length:1407
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee...ee.hhhhhhhhhhhhhhhhhhhhhh......ee.....hhhhhhhhhhhhhhh...........eeeeeeee........hhhhhhhhhhh..hhhhhhhhhhhh..eeee..eeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhh..eeeeeee..eeeeeeeehhhhhhhhhhhhhhhh.................hhhhh...hhhhhhhhhhhhhhhhh.........hhh.eeeeee......eeeee..eeeeeee.hhh......eeeee......eeeeeeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh............hhhhhheeee....eeeehhhhh........hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh.........hhhhhhhhhhhhhh...hhhhhhhhhhhh..........hhhhhh....hhhhhhhhhhhhhhhhhhhhh..hhhhh.............hhhhhhhhhhhhhh.........ee......ee.....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh......eeeeee.....hhhhh.......eeeeeeeeeee...ee..........eeeeeeeeeeeee.......hhhhhhhhhhhhhh..........eeeeeeee....eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhh...eeeee.....eeeeee.....eeeeee.eeeeee.....eeeeeeehhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhh......eee......hhhhhhhhhhhhhhhhhh...eeeeee...hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhh.eeeee.........eeeeehhhhhhhhhh.......eeeeeeeee..eeeeeeeeeeee..eee....eee...............eeeeeeeee.......hhhhhhhhhhhhh......eeeeeeee..eeeeeeeeehhhhhhhhhhh...........hhh.eeeeeeeee.....eeeee......hhhhh..........eee.......hhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4i43 B  882 GSGVMVEWLESRSFSPIPFPPLTYKNDTKILVLALEDLKDVYASKVRLNASEREELALIEEAYDNPHDTLNRIKKYLLTQRVFKPVDITPVYSVDPLEKITDAYLDQYLWYEADQRKLFPNWIKPSDSEIPPLLVYKWTQGINNLSEIWDVSRGQSAVLLETTLGEMAEKIDFTLLNRLLRLIVDPNIADYITAKNNVVINFKDMSHVNKYGLIRGLKFASFIFQYYGLVIDLLLLGQERATDLAGPANNPNEFMQFKSKEVEKAHPIRLYTRYLDRIYMLFHFEEDEGEELTDEYLAENPDPNFENSIGYNNRKCWPKDSRMRLIRQDVNLGRAVFWEIQSRVPTSLTSIKWENAFVSVYSKNNPNLLFSMCGFEVRILPRQRMEENDEGVWDLVDERTKQRTAKAYLKVSEEEIKKFDSRIRGILMASTTFTKVAAKWNTSLISLFTYFREAIVATEPLLDILVKGETRIQNRVKLGLNSKMPTRFPPAVFYTPKELGGLGMISASHILIPASDLSWSKQTDTGITHFRAGMTHEDEKLIPTIFRYITTWENEFLDSQRVWAEYATKRQEAIQQNRRLAFEELEGSWDRGIPRISTLFQRDRHTLAYDRGHRIRREFKQYSLERNSPFWWTNSHHDGKLWNLNAYRTDVIQALGGIETILEHTLFKGTGFNSWEGLFWLSQIPNRRFTLWWSPTINRANVYVGFLVQLDLTGIFLHGKIPTLKISLIQIFRAHLWQKIHESIVFDICQILDGELDVLQIESVTKETVHPRKSYKMNSSAADITMESVHEWEVSKPSLLHETNDSFKGLITNKMWFDVQLRYGDYDSHDISRYVRAKFLDYTTDNVSMYPSPTGVMIGIDLAYNMYDAYGNWFNGLKPLIQNSMRTIMKANPALYVLRERIRKGLQIYQEPFLNSSNYAELFNNDIKLFVDDTNVYRVTVHKTFEGNVATKAINGCIFTLNPKTGHLFLKIIHTSVWAGQKRLSQLAKWKTAEEVSALVRSLPKEEQPKQIIVTRKAMLDPLEVHMLDFPNIAIRPTELRLPFSAAMSIDKLSDVVMKATEPQMVLFNIYDDWLDRISSYTAFSRLTLLLRALKTNEESAKMILLSDPTITIKSYHLWPSFTDEQWITIESQMRDLILTEYGRKYNVNISALTQTESSKNEWRKSAIANTLLYLRLKNIYVSADDFVEEQNVYVLPKNLLKKFIEISDVKIQVAAFIYGMSAKDHPKVKEIKTVVLVPQLGHVGSVQISNIPDIGDLPDTEGLELLGWIHTQTEELKFMAASEVATHSKLFADKKRDCIDISIFSTPGSVSLSAYNLTDEGYQWGEENKDIMNVLSEGFEPTFSTHAQLLLSDRITGNFIIPSGNVWNYTFMGTAFNQEGDYNFKYGIPLEFYNEMHRPVHFLQFS 2396
                                   891       901       911       921       931       941       951       961       980       990      1000      1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220      1230      1240      1250      1260      1270      1283      1293      1303      1313      1323|     1335      1345      1355      1365      1375      1385      1395      1405      1415      1425      1435      1445      1455      1465      1475      1485      1495      1505      1515      1525      1535      1545      1555      1565      1575|     1607      1617      1627      1637      1647      1657      1667      1677      1687      1697      1707      1717      1727      1737      1747      1757      1767      1777      1787      1797      1807      1817      1831      1841      1851      1861      1871      1881      1891      1901      1911      1921      1931      1941      1951      1961      1971      1981      1991      2001      2011      2021      2031      2041      2051      2061      2071      2149      2159      2169      2179      2189      2199      2209      2219      2229      2239      2249      2259      2269      2279      2289      2299      2309      2319      2329      2339      2349      2359      2369      2379      2389       
                                                                                                                  970|                                                                                                                                                                                                                                                                                                     1277|                                      1323|                                                                                                                                                                                                                                                     1575|                                                                                                                                                                                                                                1826|                                                                                                                                                                                                                                                   2078|                                                                                                                                                                                                                                                         
                                                                                                                   980                                                                                                                                                                                                                                                                                                      1281                                       1326                                                                                                                                                                                                                                                      1598                                                                                                                                                                                                                                 1831                                                                                                                                                                                                                                                    2147
   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 4I43)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4I43)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4I43)

(-) Gene Ontology  (23, 28)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  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 4i43)
 
  Sites
(no "Sites" information available for 4i43)
 
  Cis Peptide Bonds
    Ile B:1488 - Pro B:1489   [ RasMol ]  
    Lys B:1014 - Pro B:1015   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit 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
  4i43
    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
  AAR2_YEAST | P32357
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  PRP8_YEAST | P33334
    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
  AAR2_YEAST | P32357
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  PRP8_YEAST | P33334
    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
        AAR2_YEAST | P32357: 3sbs 3sbt 3zef 4ilg 4ilh 4ili
        PRP8_YEAST | P33334: 2og4 3e66 3e9o 3e9p 3jcm 3sbg 3sbt 3zef 4bgd 4ilg 4ilh 4ilj 5dca 5gam 5gan 5gao 5gap 5gm6 5gmk 5lj3 5lj5 5lqw 5m52 5m5p 5mps 5mq0 5wsg

(-) Related Entries Specified in the PDB File

3zef