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

(-) Description

Title :  CRYSTAL STRUCTURE OF FULL-LENGTH YEAST PML1P
 
Authors :  S. Trowitzsch, G. Weber, R. L Hrmann, M. C. Wahl
Date :  23 Sep 08  (Deposition) - 10 Feb 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Intrinsically Unstructured Domain, Forkhead-Associated Domain (Fha) Domain, Pre-Mrna Retention And Splicing, Protein Phosphorylation, Res Complex, Mrna Processing, Mrna Splicing, Nucleus, Splicing (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Trowitzsch, G. Weber, R. Luhrmann, M. C. Wahl
Crystal Structure Of The Pml1P Subunit Of The Yeast Precursor Mrna Retention And Splicing Complex.
J. Mol. Biol. V. 385 531 2009
PubMed-ID: 19010333  |  Reference-DOI: 10.1016/J.JMB.2008.10.087

(-) Compounds

Molecule 1 - PRE-MRNA LEAKAGE PROTEIN 1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCDFDUET-1
    Expression System Strain: ROSETTA 2 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PML1, YLR016C, L1591
    Organism Common: BREWER'S YEAST,LAGER BEER YEAST,YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 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  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:108 , SER A:137 , LYS A:138BINDING SITE FOR RESIDUE SO4 A 205
2AC2SOFTWAREGLU A:179 , ARG A:181BINDING SITE FOR RESIDUE SO4 A 206
3AC3SOFTWAREARG B:108 , SER B:137 , LYS B:138BINDING SITE FOR RESIDUE SO4 B 205

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ELV)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ELV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ELV)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FHA_DOMAINPS50006 Forkhead-associated (FHA) domain profile.PML1_YEAST104-172
 		  2A:104-172
B:104-172
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FHA_DOMAINPS50006 Forkhead-associated (FHA) domain profile.PML1_YEAST104-172
 		  1A:104-172
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FHA_DOMAINPS50006 Forkhead-associated (FHA) domain profile.PML1_YEAST104-172
 		  1-
B:104-172

(-) Exons   (0, 0)

(no "Exon" information available for 3ELV)

(-) 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:145
 aligned with PML1_YEAST | Q07930 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:154
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    
           PML1_YEAST    51 KHVEPQDAISPDNYMDMLGLEARDRTMYELVIYRKNDKDKGPWKRYDLNGRSCYLVGRELGHSLDTDLDDRTEIVVADIGIPEETSSKQHCVIQFRNVRGILKCYVMDLDSSNGTCLNNVVIPGARYIELRSGDVLTLSEFEEDNDYELIFMNV 204
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhh..hhhhh..eeeeeee.hhh.....eeee.....eeeeee....---------.......eee.........eeeeeeee..eeeeeeee.......ee..ee......ee.....eee...hhhhh.eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------FHA_DOMAIN  PDB: A:104-172 UniProt: 104-172                          -------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3elv A  51 KHVEPQDAISPDNYMDMLGLEARDRTMYELVIYRKNDKDKGPWKRYDLNGRSCYLVGRELGH---------TEIVVADIGIPEETSSKQHCVIQFRNVRGILKCYVMDLDSSNGTCLNNVVIPGARYIELRSGDVLTLSEFEEDNDYELIFMNV 204
                                    60        70        80        90       100       110 |       - |     130       140       150       160       170       180       190       200    
                                                                                       112       122                                                                                  


Chain B from PDB  Type:PROTEIN  Length:144
 aligned with PML1_YEAST | Q07930 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:154
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    
           PML1_YEAST    51 KHVEPQDAISPDNYMDMLGLEARDRTMYELVIYRKNDKDKGPWKRYDLNGRSCYLVGRELGHSLDTDLDDRTEIVVADIGIPEETSSKQHCVIQFRNVRGILKCYVMDLDSSNGTCLNNVVIPGARYIELRSGDVLTLSEFEEDNDYELIFMNV 204
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhh..hhhhh..eeeeeee.........eeee.....eeeeee...----------.......eee.........eeeeeee....eeeeeee.......ee..ee......ee.....eee...hhhhh.eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------FHA_DOMAIN  PDB: B:104-172 UniProt: 104-172                          -------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3elv B  51 KHVEPQDAISPDNYMDMLGLEARDRTMYELVIYRKNDKDKGPWKRYDLNGRSCYLVGRELG----------TEIVVADIGIPEETSSKQHCVIQFRNVRGILKCYVMDLDSSNGTCLNNVVIPGARYIELRSGDVLTLSEFEEDNDYELIFMNV 204
                                    60        70        80        90       100       110|        - |     130       140       150       160       170       180       190       200    
                                                                                      111        122
   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 3ELV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ELV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ELV)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PML1_YEAST | Q07930)
molecular function
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
    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: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:0051237    maintenance of RNA location    Any process in which RNA is maintained in a location and prevented from moving elsewhere.
cellular component
    GO:0070274    RES complex    A protein complex that is required for efficient splicing, and prevents leakage of unspliced pre-mRNAs from the nucleus (named for pre-mRNA REtention and Splicing). In Saccharomyces, the complex consists of Ist3p, Bud13p, and Pml1p.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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

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
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3elv)
 
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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites 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
  3elv
    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
  PML1_YEAST | Q07930
    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
  PML1_YEAST | Q07930
    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
        PML1_YEAST | Q07930: 2jkd 2mkc 2my3 3els 5gm6 5lqw

(-) Related Entries Specified in the PDB File

3els CRYSTAL STRUCTURE OF PML1P RESIDUES 51-204