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(-) Description

Title :  CRYSTAL STRUCTURE OF S. POMBE DCP2:DCP1:EDC1 MRNA DECAPPING COMPLEX
 
Authors :  E. Valkov, S. Muthukumar, C. T. Chang, S. Jonas, O. Weichenrieder, E. Iz
Date :  31 Mar 16  (Deposition) - 18 May 16  (Release) - 15 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Hydrolase, Decapping, Mrna Decay, Evh1, Nudix (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Valkov, S. Muthukumar, C. T. Chang, S. Jonas, O. Weichenrieder, E. Izaurralde
Structure Of The Dcp2-Dcp1 Mrna-Decapping Complex In The Activated Conformation.
Nat. Struct. Mol. Biol. V. 23 574 2016
PubMed-ID: 27183195  |  Reference-DOI: 10.1038/NSMB.3232

(-) Compounds

Molecule 1 - MRNA-DECAPPING ENZYME SUBUNIT 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PNEAPG
    Expression System Taxid: 469008
    Expression System Variant: STAR
    Expression System Vector Type: PLASMID
    Gene: DCP1, SPBC3B9.21
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE
    Organism Taxid: 4896
 
Molecule 2 - MRNA DECAPPING COMPLEX SUBUNIT 2
    Chains: B
    EC Number: 3.6.1.62
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PNYC
    Expression System Taxid: 469008
    Expression System Variant: STAR
    Expression System Vector Type: PLASMID
    Gene: DCP2, SPAC19A8.12
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE
    Organism Taxid: 4896
    Strain: 972 / ATCC 24843
 
Molecule 3 - EDC1
    Chains: C
    Engineered: YES
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE
    Organism Taxid: 4896
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1FMT5Ligand/IonFORMIC ACID
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:31 , HIS A:32 , THR A:53 , ARG A:71 , HOH A:319 , ASN B:22 , LEU B:23binding site for residue FMT A 201
2AC2SOFTWAREPHE A:80 , ILE A:81 , ASN A:82 , HIS A:83 , ASN A:86 , HIS A:96 , ARG A:97 , ASN A:119binding site for residue FMT A 202
3AC3SOFTWAREGLY B:124 , PHE B:125 , LYS B:127 , MET B:221binding site for residue FMT B 301
4AC4SOFTWAREARG A:92 , ASN B:157 , GLU B:160 , HOH B:486binding site for residue FMT B 302
5AC5SOFTWAREARG B:91 , TYR B:92 , GLN B:109 , LYS B:195 , ILE B:196 , GLU B:197 , HOH B:439binding site for residue FMT B 303
6AC6SOFTWARETYR B:92 , PHE B:185 , HOH B:429 , HOH B:439 , HOH B:463 , HOH B:513binding site for residue MG B 304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5J3T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5J3T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5J3T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5J3T)

(-) Exons   (0, 0)

(no "Exon" information available for 5J3T)

(-) 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:126
                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhh..hhhhhhhh...eeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeee....eeeeeee......eeee......eeee..eeeeee...eeeeeee..hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5j3t A   2 EDENILRNAVNLQVLKFHYPEIESIIDIASHVAVYQFDVGSQKWLKTSIEGTFFLVKDQRARVGYVILNRNSPENLYLFINHPSNVHLVDRYLIHRTENQHVVGLWMFDPNDMSRIFNIVKESLLR 127
                                    11        21        31        41        51        61        71        81        91       101       111       121      


Chain B from PDB  Type:PROTEIN  Length:230
                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh.....hhhh..hhhhhhhhhhhhhhhhh.hhhh........hhhhhhhhh......hhhhhh.hhhhhhhh.......eeeeee......eeeeee...........eee......hhhhhhhhhhhhh............eeeeee..eeeeeeee..................eeeeee............hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j3t B   2 SFTNATFSQVLDDLSARFILNLPAEEQSSVERLCFQIEQAHWFYEDFIRAQNDQLPSLGLRVFSAKLFAHCPLLWKWSKVHEEAFDDFLRYKTRIPVRGAIMLDMSMQQCVLVKGWKASSGWGFPKGKIDKDESDVDCAIREVYEETGFDCSSRINPNEFIDMTIRGQNVRLYIIPGISLDTRFESRTRKEISKIEWHNLMDLPTNKFYMVIPFLAPLKKWIKKRNIANN 241
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201    || 221       231       241
                                                                                                                                                                                                                                      206|                        
                                                                                                                                                                                                                                       217                        


Chain C from PDB  Type:PROTEIN  Length:25
                                                         
               SCOP domains ------------------------- SCOP domains
               CATH domains ------------------------- CATH domains
               Pfam domains ------------------------- Pfam domains
         Sec.struct. author .eeee.................... Sec.struct. author
                 SAPs(SNPs) ------------------------- SAPs(SNPs)
                    PROSITE ------------------------- PROSITE
                 Transcript ------------------------- Transcript
                 5j3t C 155 SILYAGPTFTHSPAASNLPIPTFLH 179
                                   164       174
   Legend:   → Mismatch (orange background)
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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 5J3T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5J3T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5J3T)

(-) Gene Ontology  (29, 43)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  5j3t
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  DCP1_SCHPO | Q9P805
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  DCP2_SCHPO | O13828
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  YAQ9_SCHPO | Q10108
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 Related Entries

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

UniProtKB/Swiss-Prot
        DCP1_SCHPO | Q9P805: 2qkl 2qkm 5j3q 5j3y 5jp4 5kq1 5kq4 5n2v
        DCP2_SCHPO | O13828: 2a6t 2qkl 2qkm 4a54 5j3y 5kq1 5kq4 5n2v
        YAQ9_SCHPO | Q10108: 5j3q 5jp4 5n2v

(-) Related Entries Specified in the PDB File

5j3q CRYSTAL STRUCTURE OF S. POMBE DCP1:EDC1 MRNA DECAPPING COMPLEX
5j3y CRYSTAL STRUCTURE OF S. POMBE DCP2:DCP1 MRNA DECAPPING COMPLEX