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(-) Description

Title :  CRYSTAL STRUCTURE OF YEAST PML1P, RESIDUES 51-204
 
Authors :  S. Trowitzsch, G. Weber, R. Luehrmann, M. C. Wahl
Date :  23 Sep 08  (Deposition) - 10 Feb 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (6x)
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
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCDFDUET-1
    Expression System Strain: ROSETTA2 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 51 TO 204
    Gene: PML1, YLR016C, L1591
    Organism Common: BREWER'S YEAST,LAGER BEER YEAST,YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (6x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL4Ligand/IonGLYCEROL
3MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL4Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 24)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL24Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:128 , HOH A:210 , HOH A:214BINDING SITE FOR RESIDUE MG A 1
2AC2SOFTWAREARG A:176 , HOH A:357BINDING SITE FOR RESIDUE CL A 205
3AC3SOFTWAREMET A:77 , TYR A:78 , GLU A:79 , LYS A:88 , GLY A:91 , ASP A:97 , ASN A:99 , ILE A:124BINDING SITE FOR RESIDUE GOL A 206
4AC4SOFTWARELYS A:51 , ASP A:62 , ARG A:75 , MET A:77 , ASP A:89 , ASP A:97 , ASN A:99 , GOL A:208 , HOH A:216 , HOH A:254BINDING SITE FOR RESIDUE GOL A 207
5AC5SOFTWARELYS A:51 , ASP A:62 , ASP A:66 , ARG A:75 , GOL A:207 , HOH A:341 , HOH A:372BINDING SITE FOR RESIDUE GOL A 208
6AC6SOFTWAREVAL A:148 , ARG A:149 , ASN A:169 , VAL A:185 , THR A:187 , GLU A:192 , GLU A:198 , HOH A:218 , HOH A:271 , HOH A:276 , HOH A:335 , HOH A:352BINDING SITE FOR RESIDUE GOL A 209

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FHA_DOMAINPS50006 Forkhead-associated (FHA) domain profile.PML1_YEAST104-172  1A: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, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FHA_DOMAINPS50006 Forkhead-associated (FHA) domain profile.PML1_YEAST104-172  6A:104-172

(-) Exons   (0, 0)

(no "Exon" information available for 3ELS)

(-) 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.hhhhhh..eeee.....eeeeee....---------.......eee.........eeeeeeee..eeeeeeee.......ee..ee......ee....eeee...hhhhh.eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------FHA_DOMAIN  PDB: A:104-172 UniProt: 104-172                          -------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3els A  51 KHVEPQDAISPDNYMDMLGLEARDRTMYELVIYRKNDKDKGPWKRYDLNGRSCYLVGRELGH---------TEIVVADIGIPEETSSKQHCVIQFRNVRGILKCYVMDLDSSNGTCLNNVVIPGARYIELRSGDVLTLSEFEEDNDYELIFMNV 204
                                    60        70        80        90       100       110 |       - |     130       140       150       160       170       180       190       200    
                                                                                       112       122
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 3ELS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (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.

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  PML1_YEAST | Q07930
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 Related Entries

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

UniProtKB/Swiss-Prot
        PML1_YEAST | Q07930: 2jkd 2mkc 2my3 3elv 5gm6 5lqw

(-) Related Entries Specified in the PDB File

3elv