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(-)Asym./Biol. Unit
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(-) Description

Title :  CRYSTAL STRUCTURE OF S. POMBE DCP1/DCP2 IN COMPLEX WITH H. SAPIENS PNRC2
 
Authors :  J. S. Mugridge, M. Ziemniak, J. Jemielity, J. D. Gross
Date :  05 Jul 16  (Deposition) - 05 Oct 16  (Release) - 16 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Decapping Mrna Decay Nudix Cap Analog, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. S. Mugridge, M. Ziemniak, J. Jemielity, J. D. Gross
Structural Basis Of Mrna-Cap Recognition By Dcp1-Dcp2.
Nat. Struct. Mol. Biol. V. 23 987 2016
PubMed-ID: 27694842  |  Reference-DOI: 10.1038/NSMB.3301

(-) Compounds

Molecule 1 - MRNA-DECAPPING ENZYME SUBUNIT 1
    Chains: A, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21*DE3
    Expression System Taxid: 469008
    Gene: DCP1, SPBC3B9.21
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE (STRAIN 972 / ATCC 24843)
    Organism Taxid: 284812
    Strain: 972 / ATCC 24843
 
Molecule 2 - PROLINE-RICH NUCLEAR RECEPTOR COACTIVATOR 2
    Chains: C, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21*DE3
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 72-102
    Gene: PNRC2, HSPC208
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: C-TERMINUS OF PNRC2 IS LINKED TO N-TERMINUS OF DCP2 BY GGGGS LINKER
 
Molecule 3 - MRNA DECAPPING COMPLEX SUBUNIT 2
    Chains: B, E
    EC Number: 3.-.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21*DE3
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 1-244
    Gene: DCP2, SPAC19A8.12
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE (STRAIN 972 / ATCC 24843)
    Organism Taxid: 284812
    Other Details: GGGGS LINKER AT THE N-TERMINUS OF DCP2 IS CONNECTED TO THE C-TERMINUS OF PNRC2
    Strain: 972 / ATCC 24843

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5KQ1)

(-) Sites  (0, 0)

(no "Site" information available for 5KQ1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5KQ1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5KQ1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5KQ1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5KQ1)

(-) Exons   (0, 0)

(no "Exon" information available for 5KQ1)

(-) 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 ..hhhhhhhhhhhhhhhhh...eeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeee....eeeeeee......eeeee.....eeee..eeeee.....eeeeee..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5kq1 A   1 MEDENILRNAVNLQVLKFHYPEIESIIDIASHVAVYQFDVGSQKWLKTSIEGTFFLVKDQRARVGYVILNRNSPENLYLFINHPSNVHLVDRYLIHRTENQHVVGLWMFDPNDMSRIFNIVKESLL 126
                                    10        20        30        40        50        60        70        80        90       100       110       120      


Chain B from PDB  Type:PROTEIN  Length:236
                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhh.....hhhhh.hhhhhhhhhhhhhhhhh.hhhh........hhhhhhhhhhh..hhhh..hhhhhhhhhhhhh...eeeeeeee......eeeeee...........eee......hhhhhhhhhhhhh............eeeeee..eeeeeeee...............eeeeee....................hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kq1 B   0 SMSFTNATFSQVLDDLSARFILNLPAEEQSSVERLCFQIEQAHWFYEDFIRAQNDQLPSLGLRVFSAKLFAHCPLLWKWSKVHEEAFDDFLRYKTRIPVRGAIMLDMSMQQCVLVKGWKASSGWGFPKGKIDKDESDVDCAIREVYEETGFDCSSRINPNEFIDMTIRGQNVRLYIIPGISLDTRFESREISKIEWHNLMDLPTFKKNKPMKNKFYMVIPFLAPLKKWIKKRNIAN 240
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       192       202       212|      224       234      
                                                                                                                                                                                                                      188|                 212|                         
                                                                                                                                                                                                                       192                  215                         


Chain C from PDB  Type:PROTEIN  Length:22
                                                      
               SCOP domains ---------------------- SCOP domains
               CATH domains ---------------------- CATH domains
               Pfam domains ---------------------- Pfam domains
         Sec.struct. author ............hhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------- SAPs(SNPs)
                    PROSITE ---------------------- PROSITE
                 Transcript ---------------------- Transcript
                 5kq1 C 100 EPPSPSVLPKPPSHWVPVSFNP 121
                                   109       119  


Chain D from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh...eeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeee....eeeeeee......eeeee.....eeee..eeeee.....eeeeee..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kq1 D   1 MEDENILRNAVNLQVLKFHYPEIESIIDIASHVAVYQFDVGSQKWLKTSIEGTFFLVKDQRARVGYVILNRNSPENLYLFINHPSNVHLVDRYLIHRTENQHVVGLWMFDPNDMSRIFNIVK 122
                                    10        20        30        40        50        60        70        80        90       100       110       120  


Chain E from PDB  Type:PROTEIN  Length:235
                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhh.....hhhh..hhhhhhhhhhhhhhhhh.hhh.........hhhhhhhhhhh............hhhhhhh...eeeeeeee......eeeeeee..........eee......hhhhhhhhhhhhh............eeeeee..eeeeeeee..............eeeeeeee...................hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kq1 E   0 SMSFTNATFSQVLDDLSARFILNLPAEEQSSVERLCFQIEQAHWFYEDFIRAQNDQLPSLGLRVFSAKLFAHCPLLWKWSKVHAFDDFLRYKTRIPVRGAIMLDMSMQQCVLVKGWKASSGWGFPKGKIDKDESDVDCAIREVYEETGFDCSSRINPNEFIDMTIRGQNVRLYIIPGISLDTRFESRTEISKIEWHNLMDLPTFKKNKMKNKFYMVIPFLAPLKKWIKKRNIANN 241
                                     9        19        29        39        49        59        69        79  ||    91       101       111       121       131       141       151       161       171       181       193       203       216       226       236     
                                                                                                             82|                                                                                                     189|                211|                          
                                                                                                              85                                                                                                      192                 215                          


Chain F from PDB  Type:PROTEIN  Length:21
                                                     
               SCOP domains --------------------- SCOP domains
               CATH domains --------------------- CATH domains
               Pfam domains --------------------- Pfam domains
         Sec.struct. author ..................... Sec.struct. author
                 SAPs(SNPs) --------------------- SAPs(SNPs)
                    PROSITE --------------------- PROSITE
                 Transcript --------------------- Transcript
                 5kq1 F 101 PPSPSVLPKPPSHWVPVSFNP 121
                                   110       120
   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 5KQ1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5KQ1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5KQ1)

(-) Gene Ontology  (29, 47)

Asymmetric/Biological Unit(hide GO term definitions)

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(no "Cis Peptide Bonds" information available for 5kq1)
 

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  DCP1_SCHPO | Q9P805
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  DCP2_SCHPO | O13828
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  PNRC2_HUMAN | Q9NPJ4
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 Related Entries

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

UniProtKB/Swiss-Prot
        DCP1_SCHPO | Q9P805: 2qkl 2qkm 5j3q 5j3t 5j3y 5jp4 5kq4 5n2v
        DCP2_SCHPO | O13828: 2a6t 2qkl 2qkm 4a54 5j3t 5j3y 5kq4 5n2v
        PNRC2_HUMAN | Q9NPJ4: 4b6h 5kq4

(-) Related Entries Specified in the PDB File

5kq4