Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF AN AAR2P S253E PHOSPHOMIMETIC MUTANT PROTEIN
 
Authors :  G. Weber, C. Heroven, K. F. Santos, M. C. Wahl
Date :  31 Dec 12  (Deposition) - 13 Mar 13  (Release) - 27 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  U5 Snrnp Assembly, Aar2, Prp8, Splicing (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Weber, V. F. Cristao, K. F. Santos, S. M. Jovin, A. C. Heroven, N. Holton, R. Luhrmann, J. D. Beggs, M. C. Wahl
Structural Basis For Dual Roles Of Aar2P In U5 Snrnp Assembly.
Genes Dev. V. 27 525 2013
PubMed-ID: 23442228  |  Reference-DOI: 10.1101/GAD.213207.113

(-) Compounds

Molecule 1 - A1 CISTRON-SPLICING FACTOR AAR2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: AAR2, YBL074C, YBL06.06, YBL0611
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 4ILI)

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:251 -A:292
2B:251 -B:292

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys A:299 -Asn A:300
2Lys B:299 -Asn B:300

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ILI)

(-) Sequences/Alignments

Asymmetric 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:290
                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.......eeeee..eeeee.......eee.......eeeeeee.......eeeeehhhhh.eeeeee....eeeeee..hhhhhhhhhh.......eee.......hhhhhhh...hhhhhhhhh.......eeee....hhhhhhhh.......................hhhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh.....hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ili A   2 NTVPFTSAPIEVTIGIDQYSFNVKENQPFHGIKDIPIGHVHVIHFQHADNSSMRYGYWFDCRMGNFYIQYDPKDGLYKMMEERDGAKFENIVHNFKERQMMVSYPKIDEDDTWYNLTEFVQMDKIRKIVRKDENQFSYVDSSMTTVQENELSSSSSDPAHSLNYTVINFKSDKSYYLNTVMLQGIFKNSSNYFGELQFAFLNAMFFGNYGSSLQWHAMIELICSEATVPKHMLDKLDEILYYQIKTLPEQYSDILLNERVWNICLYSSFQKNSLHNTEKIMENKYPELLG 318
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151     ||174       184||     208       218       228       238       248       258       268       278       288       298       308       318
                                                                                                                                                                                     157|           185|                                                                                                                      
                                                                                                                                                                                      171            200                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:292
                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.......eeeee..ee..........eeeee.....eeeeeee.......eeeeehhhhheeeeee......eeeeee.hhhhhhhhhhhhhhh...ee.......hhhhhhh...hhhhhhhhh.......eee....ee...............ee................hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh.....hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ili B   1 MNTVPFTSAPIEVTIGIDQYSFNVKENQPFHGIKDIPIGHVHVIHFQHADNSSMRYGYWFDCRMGNFYIQYDPKDGLYKMMEERDGAKFENIVHNFKERQMMVSYPKIDEDDTWYNLTEFVQMDKIRKIVRKDENQFSYVDSSMTTVQENELSSSSSDPAHSLNYTVINFMEDFLDKSYYLNTVMLQGIFKNSSNYFGELQFAFLNAMFFGNYGSSLQWHAMIELICSEATVPKHMLDKLDEILYYQIKTLPEQYSDILLNERVWNICLYSSFQKNSLHNTEKIMENKYPEL 316
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150      |173       183|      204       214       224       234       244       254       264       274       284       294       304       314  
                                                                                                                                                                                      157|         183|                                                                                                                         
                                                                                                                                                                                       171          195
   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 4ILI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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 4ili)
 
  Sites
(no "Sites" information available for 4ili)
 
  Cis Peptide Bonds
    Lys A:299 - Asn A:300   [ RasMol ]  
    Lys B:299 - Asn B:300   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 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
  4ili
    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
 
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)

 Related Entries

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

UniProtKB/Swiss-Prot
        AAR2_YEAST | P32357: 3sbs 3sbt 3zef 4i43 4ilg 4ilh

(-) Related Entries Specified in the PDB File

4ilg 4ilh 4ilj