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(-) Description

Title :  STRUCTURE OF THE RRP6-RRP47 INTERACTION
 
Authors :  B. Schuch, E. Conti
Date :  14 Sep 14  (Deposition) - 29 Oct 14  (Release) - 10 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  Rrp6-Rrp47 Complex, Nuclear Exosome, Rna Degradation, Rna Processing, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Schuch, M. Feigenbutz, D. L. Makino, S. Falk, C. Basquin, P. Mitchell, E. Conti
The Exosome-Binding Factors Rrp6 And Rrp47 Form A Composite Surface For Recruiting The Mtr4 Helicase.
Embo J. V. 33 2829 2014
PubMed-ID: 25319414  |  Reference-DOI: 10.15252/EMBJ.201488757

(-) Compounds

Molecule 1 - EXOSOME COMPLEX EXONUCLEASE RRP6
    Chains: A, C, E
    EC Number: 3.1.13.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-111
    Gene: RRP6, UNC733, YOR001W
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: RIBOSOMAL RNA-PROCESSING PROTEIN 6
 
Molecule 2 - EXOSOME COMPLEX PROTEIN LRP1
    Chains: B, D, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-133
    Gene: LRP1, RRP47, YC1D, YHR081W
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: LIKE AN RRNA PROCESSING PROTEIN 1,YEAST C1D DOMAIN- CONTAINING PROTEIN,RRNA PROCESSING PROTEIN 47

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB    
Biological Unit 2 (1x):   CD  
Biological Unit 3 (1x):     EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:3 , GLU A:4 , ARG A:18 , SER D:41binding site for residue SO4 A 201
2AC2SOFTWAREARG B:96 , LYS B:99 , HOH B:308binding site for residue SO4 B 201
3AC3SOFTWARESER B:41 , ILE C:14 , ARG C:18binding site for residue SO4 C 201
4AC4SOFTWAREILE C:103 , ARG D:96 , LYS D:99 , SER D:100binding site for residue SO4 D 201

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1E:101 -E:101

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4WFC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WFC)

(-) 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:95
                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 4wfc A   3 SENPDVLLSRVINVVRAASSLASQDVDFYKNLDRGFSKDLKSKADKLADMANEIILSIDEHHESDLWNNFGNIMDNLLEMSDHSLDKLNCAINSK 106
                                    12        22        32        42        52        62  ||    81        91       101     
                                                                                         65|                               
                                                                                          75                               


Chain B from PDB  Type:PROTEIN  Length:118
                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 4wfc B   3 DIEKIKPYVRSFSKALDELKPEIEKLTSKSLDEQLLLLSDERAKLELINRYAYVLSSLMFANMKVLGVKDMSPILGELKRVKSYMDKAKQYDNRITKSNEKSQAEQEKAKNIISNVLD 120
                                    12        22        32        42        52        62        72        82        92       102       112        


Chain C from PDB  Type:PROTEIN  Length:93
                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4wfc C   7 DVLLSRVINVVRAASSLASQDVDFYKNLDRGFSKDLKSKADKLADMANEIILSIDEHHEDISDLWNNFGNIMDNLLEMSDHSLDKLNCAINSK 106
                                    16        26        36        46        56        73        83        93       103   
                                                                                     65|                                 
                                                                                      73                                 


Chain D from PDB  Type:PROTEIN  Length:98
                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 4wfc D   5 EKIKPYVRSFSKALDELKPEIEKLTSKSLDEQLLLLSDERAKLELINRYAYVLSSLMFANMKVLGVKDMSPILGELKRVKSYMDKAKQYDNRITKSNE 102
                                    14        24        34        44        54        64        74        84        94        


Chain E from PDB  Type:PROTEIN  Length:70
                                                                                                      
               SCOP domains ---------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                 4wfc E   5 NPDVLLSRVINVVRAASSLASQLKSKADKLADMANEIILSIDWNNFGNIMDNLLEMSDHSLDKLNCAINS 105
                                    14        24 ||     49        59 ||     85        95       105
                                                26|                 61|                           
                                                 42                  78                           


Chain F from PDB  Type:PROTEIN  Length:93
                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4wfc F  10 YVRSFSKALDELKPEIEKLTSKSLDEQLLLLSDERAKLELINRYAYVLSSLMFANMKVLGVKDMSPILGELKRVKSYMDKAKQYDNRITKSNE 102
                                    19        29        39        49        59        69        79        89        99
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 4WFC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (39, 52)

Asymmetric Unit(hide GO term definitions)

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  4wfc
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  RRP6_YEAST | Q12149
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 Related Entries

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

UniProtKB/Swiss-Prot
        LRP1_YEAST | P38801: 4wfd 5c0w
        RRP6_YEAST | Q12149: 1m0y 2hbj 2hbk 2hbl 2hbm 4ifd 4oo1 4wfd 5c0w 5c0x 5c0y 5k36

(-) Related Entries Specified in the PDB File

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